Swissbiopics Examples

Swissbiopics

Animal Cell: Cytosol

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Protein located outside the cell membrane(s).Secreted The extracellular space is the space outside of the cell membrane but part of a multicellular organism. The term is typically used for a secreted protein that remains associated with the cell, e.g. as part of the extracellular matrix. It is not used for a protein that is secreted into the blood stream (or other body fluids) of eukaryotic, multicellular organisms, such as insulin or fibroblast growth factors.Extracellular space The extracellular matrix (ECM) is a vague term used to refer to all the material surrounding cells in a multicellular organism, except circulating fluids such as blood or lymph. In some cases, the ECM accounts for more of the organism's bulk than its cells. In plants, arthropods and fungi the ECM is primarily composed of nonliving material such as cellulose or chitin. In vertebrates the ECM consists of a complex network including the basement membrane, collage, elastin, proteoglycans and hyaluronan.Extracellular matrix http://purl.uniprot.org/locations/111 http://purl.uniprot.org/locations/112 Exosomes are 30-120 nm microvesicles of endocytic origin secreted by most cell types and found in abundance in body fluids, including blood, saliva, urine, and breast milk. They contain various molecular constituents of their cell of origin, including proteins and nucleic acids, and carry this cargo between diverse locations in the body. These microvesicles form by budding into the lumen of the multivesicular bodies (MVBs) and are released to extracellular fluids by fusion of MVBs with the plasma membrane.Extracellular exosome http://purl.uniprot.org/locations/466 http://purl.uniprot.org/locations/243 The cytoplasm is the content of a cell within the plasma membrane and, in eukaryotics cells, surrounding the nucleus. This three-dimensional, jelly-like lattice interconnects and supports the other solid structures. The cytosol (the soluble portion of the cytoplasm outside the organelles) is mostly composed of water and many low molecular weight compounds. In eukaryotes, the cytoplasm also contains a network of cytoplasmic filaments (cytoskeleton).Cytoplasm The cytosol is the unstructured aqueous phase of the cytoplasm excluding organelles, membranes, and insoluble cytoskeletal components.Cytosol http://purl.uniprot.org/locations/91 http://purl.uniprot.org/locations/86 The cell cortex is the cytoplasmic region under the cell membrane.Cell cortex http://purl.uniprot.org/locations/138 The perinuclear region is the cytoplasmic region just around the nucleus.Perinuclear region http://purl.uniprot.org/locations/198 The cytoskeleton is a dynamic three-dimensional filamentous structure in the cytoplasm. Its roles include maintenance of cell shape, cell movement (in eukaryotes), cytokinesis, and the organization of organelles or organelle-like structures within the cell. The cytoskeleton includes microfilaments (actin-like proteins), microtubules (tubulin-like proteins), the intermediate filaments (mostly in eukaryotes) and the MinD-ParA proteins, which appear to be unique to prokaryotes.Cytoskeleton Stress fibers are contractile actomyosin bundles found in non-muscle cells, in eukaryotes, mostly in animals. They are composed of bundles of 10 to 30 actin filaments (microfilaments), crosslinked by alpha-actinin, and non-muscle myosin. They are often anchored to focal adhesions, that connect the extracellular matrix to the actin cytoskeleton. Stress fibers play an essential role in cell contractility, governing cell morphology, adhesion, and migration. In non-motile cells, stress fibers are usually thick and relatively stable. By contrast, highly motile cells typically contain fewer, thinner and more dynamic stress fibers. Stress fibers can be divided into at least 4 different categories : dorsal and ventral stress fibers, transverse arcs and the perinuclear actin cap.Stress fiber http://purl.uniprot.org/locations/501 The microtubule organizing center (MTOC) is an intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules.Microtubule organizing center The centrosome is a microtubule organizing center (MTOC) responsible for the nucleation and organisation of microtubules. It is composed of two orthogonally arranged centrioles, each one having a barrel shaped microtubule structure, and their surrounding pericentriolar material (PCM).Centrosome The centriole is a barrel-shaped microtubule-based structure. A pair of centrioles, embedded in the so-called pericentriolar material, constitute the centrosome, a microtubule organizing center of an eukaryotic cell. Centrioles are barrel-shaped microtubule-based structures organized in a 9-fold radial symmetry. Centriolar microtubule arrays usually consist of triplet microtubules, although doublets or singlets are present in some species. Centrioles are structurally related to (and often interconvertible with) basal bodies, the organelles required for the assembly of a cilium or flagellum.Centriole http://purl.uniprot.org/locations/46 Centriolar satellites are nonmembranous, electron-dense and spherical cytoplasmic granules of about 70-100 nm in diameter, occurring around centrosomes in most vertebrate cell types. They contain a number of centrosomal proteins. Centriolar satellites have the ability to move along microtubules, toward their minus ends, i.e. toward centrosomes. Their number increase during interphase and decrease during mitosis.Centriolar satellite http://purl.uniprot.org/locations/485 http://purl.uniprot.org/locations/48 http://purl.uniprot.org/locations/484 http://purl.uniprot.org/locations/90 The cell membrane is the selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the cell inner membrane in prokaryotes with 2 membranes.Cell membrane http://purl.uniprot.org/locations/39 The outermost side of the cell.Cell surface http://purl.uniprot.org/locations/310 The nucleus is the most obvious organelle in any eukaryotic cell. It is a membrane-bound organelle surrounded by double membranes which contains most of the cell's genetic material. It communicates with the surrounding cytosol via numerous nuclear pores.Nucleus The nucleoplasm is a highly viscous liquid contained within the nucleus that surrounds the chromosomes and other subnuclear organelles. A network of fibers known as the nuclear matrix can also be found in the nucleoplasm.Nucleoplasm http://purl.uniprot.org/locations/190 The membrane surrounding the nucleus. This term is used when it is not known if the protein is found in or associated with the inner or outer nuclear membrane.Nucleus membrane http://purl.uniprot.org/locations/182 The nucleolus is a non-membrane bound nuclear compartment found in eukaryotic cells which is the site of ribosome biogenesis. The interphase nucleolus is organized around the tandemly repeated genes for preribosomal RNA (rRNA). It is composed of at least 2 sub-compartments: the dense fibrillar component (DFC, also called pars fibrosa) and the granular component (GC or pars granulosa). The DFC contains newly synthesized preribosomal RNA and a collection of proteins; the GC is made up of nearly completed preribosomal particles destined for the cytoplasm. In most metazoans, but generally not in lower eukaryotes, a third component, the fibrillar center (FC), can be seen. Plant and animal nuclei can contain more than one nucleolus.Nucleolus http://purl.uniprot.org/locations/188 Nuclear body is a collective term for several nuclear, extra-nucleolar, non-membrane-bound sub-compartments, including, but not limited to Cajal bodies, Gemini of Cajal bodies (gems), nuclear speckles and PML bodies. Nuclear bodies are visible as distinct spots in the nucleoplasm. They can vary in number and size depending on the cell line and the type of nuclear body.Nuclear body The nuclear Cajal bodies (CBs) are small subnuclear membraneless organelles present either free in the nucleoplasm and/or physically associated to specific regions of chromatin. CBs contain newly assembled small nuclear ribonucleoproteins (snRNPs) and small nucleolar ribonucleoproteins (snoRNPs) particles, which are involved in pre-mRNA splicing and in ribosomal RNA processing, respectively. Mammalian nucleus in interphase, show 2-6 CBs, as irregular, punctuate structures, which vary in size and shape and which are often juxtaposed to nucleoli. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called coiled body. Structures similar to CBs have been identified in the amphibian oocyte nucleus (called sphere organelles) and in insect (called endobodies). CBs are motile and dynamic structures. Both their protein and RNA-protein components can cycle continuously between CBs and other nuclear locations depending on the transcriptional state of the cell.Cajal body http://purl.uniprot.org/locations/31 The PML bodies are dynamic nuclear protein aggregates interspersed between chromatin. These punctate nuclear structures are call PML bodies because the PML gene is essential for their formation. These discrete nuclear foci, 0.2-1.0 micrometer wide, are present in most mammalian cell nuclei and typically number 1 to 30 bodies per nucleus, depending on the cell type, cell-cycle phase and differentiation stage. Recent evidence implies that, although they appear to be uniform, PML-NBs are structurally and functionally heterogeneous and are dynamic structures.PML body http://purl.uniprot.org/locations/465 Gems are nuclear bodies, often found paired or juxtaposed to Cajal bodies, called gems for "gemini of CBs". It is not clear if Cajal bodes and gems are distinct nuclear bodies or if they should be considered as two manifestations of the same structure.Gem http://purl.uniprot.org/locations/127 The nuclear speckles are small subnuclear membraneless organelles or structures, also called the splicing factor (SF) compartments that correspond to nuclear domains located in interchromatin regions of the nucleoplasm of mammalian cells. Protein found in speckles serves as a reservoir of factors that participate in transcription and pre-mRNA processing. Speckles appear, at the immunofluorescence-microscope level, as irregular, punctuate structures, which vary in size and shape. Usually 25-50 speckles are observed per interphase mammalian nucleus. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called interchromatin granules clusters (IGCs). Speckles are dynamic structures. Both their protein and RNA-protein components can cycle continuously between speckles and other nuclear locations depending on the transcriptional state of the cell. Structures similar to nuclear speckles have been identified in the amphibian oocyte nucleus (called B snurposomes) and in Drosophila melanogaster embryos, but not in yeast.Nucleus speckle http://purl.uniprot.org/locations/186 http://purl.uniprot.org/locations/494 The nuclear lamina is a meshwork of intermediate filament proteins called lamins and lamin-binding proteins that are embedded in the inner nuclear membrane.Nucleus lamina http://purl.uniprot.org/locations/180 http://purl.uniprot.org/locations/191The inner membrane of the nucleus is the membrane which separates the nuclear matrix from the intermembrane space. In mammals, the inner nuclear membrane is associated with heterochromatin and the nuclear lamina.Nucleus inner membraneThe outer membrane of the nucleus is the membrane facing the cytoplasm. In mammals, the outer nuclear membrane is continuous in many places with the rough endoplasmic reticulum and is dotted with ribosomes.Nucleus outer membrane The mitochondrion is a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. The size and coding capacity of the mitochondrial DNA varies considerably in different organisms, and encodes rRNAs, tRNAs and essential mitochondrial proteins.Mitochondrion The matrix of a mitochondrion is the mitochondrion internal spaces enclosed by the inner membrane. Several of the steps in cellular respiration occur in the matrix due to its high concentration of enzymes.Mitochondrion matrix http://purl.uniprot.org/locations/170 The mitochondrial envelope comprises the inner and outer mitochondrial membrane including the intermembrane space.Mitochondrion envelope The membrane surrounding a mitochondrion. This term is used when it is not known if the protein is found in or associated with the inner or outer mitochondrial membrane.Mitochondrion membrane The outer membrane of a mitochondrion is the mitochondrial membrane facing the cytoplasm.Mitochondrion outer membrane http://purl.uniprot.org/locations/172 The inner membrane of a mitochondrion is the membrane which separates the mitochondrial matrix from the intermembrane space.Mitochondrion inner membrane http://purl.uniprot.org/locations/168 http://purl.uniprot.org/locations/171 http://purl.uniprot.org/locations/167 http://purl.uniprot.org/locations/173 The endoplasmic reticulum (ER) is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products. The membrane is a continuation of the outer nuclear membrane, it encloses the cytosol cisternal spaces (or internal lumen), which are continuous with the nuclear periplasmic space. The ER sustains many general functions, including protein synthesis, protein modification, protein folding, insertion of membrane proteins, sequestration of calcium, production of phospholipids and steroids and transport of proteins destined for membranes and secretion.Endoplasmic reticulum The smooth endoplasmic reticulum (SER) is the portion of the ER which is free of ribosomes.Smooth endoplasmic reticulum http://purl.uniprot.org/locations/248The membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membrane The rough endoplasmic reticulum (RER) is the portion of the ER which is covered with ribosomes.Rough endoplasmic reticulum http://purl.uniprot.org/locations/235The membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane http://purl.uniprot.org/locations/95The membrane surrounding the endoplasmic reticulum (ER). The endoplasmic reticulum is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products.Endoplasmic reticulum membraneThe membrane surrounding the microsome.Microsome membraneThe membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membraneThe membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane The Golgi apparatus is a series of flattened, cisternal membranes and similar vesicles usually arranged in close apposition to each other to form stacks. In mammalian cells, the Golgi apparatus is juxtanuclear, often pericentriolar. The stacks are connected laterally by tubules to create a perinuclear ribbon structure, the 'Golgi ribbon'. In plants and lower animal cells, the Golgi exists as many copies of discrete stacks dispersed throughout the cytoplasm. The Golgi is a polarized structure with, in most higher eukaryotic cells, a cis-face associated with a tubular reticular network of membranes facing the endoplasmic reticulum, the cis-Golgi network (CGN), a medial area of disk-shaped flattened cisternae, and a trans-face associated with another tubular reticular membrane network, the trans-Golgi network (TGN) directed toward the plasma membrane and compartments of the endocytic pathway. The Golgi apparatus receives the entire output of de novo synthesized polypeptides from the ER, and functions to posttranslationally process and sort them within vesicles destined to their proper final destination (e.g. plasma membrane, endosomes, lysosomes).Golgi apparatus The trans-Golgi network is a highly dynamic series of interconnected tubules and vesicles at the trans face of the Golgi stack. The trans-Golgi network functions in the processing and sorting of glycoproteins and glycolipids at the interface of the biosynthetic and endosomal pathways. The generation and maintenance of apical and basolateral membranes rely on sorting events that occur in the TGN.trans-Golgi network http://purl.uniprot.org/locations/266The membrane surrounding the trans-Golgi network.trans-Golgi network membrane The Golgi stack consist of a series of flattened curved and parallel series saccules, called cisternae or dictyosomes, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.Golgi stack http://purl.uniprot.org/locations/135The membrane surrounding the Golgi stack.Golgi stack membrane The cis-Golgi network is an extensive tubulovesicular network bound to the cis face of the Golgi stack and which function is to receive process the biosynthetic output from the ER.cis-Golgi network http://purl.uniprot.org/locations/67The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membrane http://purl.uniprot.org/locations/132The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membraneThe membrane surrounding the Golgi apparatus.Golgi apparatus membraneThe membrane surrounding the Golgi stack.Golgi stack membraneThe membrane surrounding the trans-Golgi network.trans-Golgi network membrane A cell projection is a cell protrusion such as pseudopodium, filopodium, lamellipodium, growth cone, flagellum, acrosome, axon, or bacterial comet tail. These membrane-cytoskeleton-coupled processes are involved in many biological functions, such as cell motility, cancer-cell invasion, endocytosis, phagocytosis, exocytosis, pathogen infection, neurite extension and cytokinesis.Cell projection The podosome is a ring-like cell protrusion which mediates cell-extracellular matrix interactions. Podosomes are composed of an actin-bundle core, flanked by a ring containing adhesion proteins connected to the core via dome-like radial actin fibers. Podosomes are rich in actin filaments, matrix-degrading enzymes, focal adhesion molecules and molecules involved in vesicle trafficking. These structures protrudes into the extracellular matrix and are essential for invasion and metastasis. Classical podosomes are highly dynamic structures formed by cell types of monocytic origin, such as macrophages, dendritic cells, and osteoclasts.Podosome http://purl.uniprot.org/locations/295 The filopodium is a thin, tubular, finger-like cell protrusion filled with straight bundled, crosslinked actin filaments having their barbed ends directed towards the cell membrane. Filopodium are observed at the advancing front of the migrating cell and are implicated in cell motility as well as in cell-substrate adhesion. Filopodia explore the environment and form nascent adhesive structures in response to external signaling cues. These long and highly dynamic protrusions, which can extend and retract, are involved in mesenchymal migration. They are observed in many cell types, such as amoebae, keratinocytes, fibroblasts and in neurite growth cones.Filopodium http://purl.uniprot.org/locations/286 The invadopodium is a localized and persitent cell protrusion similar to the highly dynamic podosome, but larger. These structures protrudes into the extracellular matrix. Invadopodial protrusions are enriched in integrins, tyrosine kinase signaling machinery, soluble and membrane proteases including matrix metalloproteases, actin and actin-associated proteins. Essential for physiological and pathological cell invasion and metastasis these structures are involved in focalized degradation of the extracellular matrix. Invadopodia form underneath the cell body, often close to the nucleus and proximal to the Golgi complex, and are rarely found at the cell periphery. Their half-life is quite extended. As invadopodia and podosomes are similar in appearance, location and composition, it is likely that a thin line separates these two entities in time and function.Invadopodium http://purl.uniprot.org/locations/148 The cilium is a cell surface projection found at the surface of a large proportion of eukaryotic cells. The two basic types of cilia, motile (alternatively named flagella) and non-motile, collectively perform a wide variety of functions broadly encompassing cell/fluid movement and sensory perception. Their most prominent structural component is the axoneme which consists of nine doublet microtubules, with all motile cilia - except those at the embryonic node - containing an additional central pair of microtubules. The axonemal microtubules of all cilia nucleate and extend from a basal body, a centriolar structure most often composed of a radial array of nine triplet microtubules. In most cells, basal bodies associate with cell membranes and cilia are assembled as 'extracellular' membrane-enclosed compartments.Cilium The basal body is a barrel-shaped microtubule-based structure required for the formation of cilia. Basal bodies, structuraly related to and often interconvertible with centrioles, serves as a nucleation site for axoneme growth.Cilium basal body http://purl.uniprot.org/locations/87 The cilium axoneme is the most prominent structural component of the cilium. It consists of nine doublet microtubules, with all motile cilia - except those at the embryonic node - containing an additional central pair of microtubules. The axonemal microtubules of all cilia nucleate and extend from a basal body, a centriolar structure most often composed of a radial array of nine triplet microtubules. In most cells, basal bodies associate with cell membranes and cilia are assembled as 'extracellular' membrane-enclosed compartments.Cilium axoneme http://purl.uniprot.org/locations/304 http://purl.uniprot.org/locations/66 http://purl.uniprot.org/locations/280 The hydrogenosome is a redox organelle of anaerobic unicellular eukaryotes which contains hydrogenase and produces hydrogen and ATP by glycolysis. They are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Most hydrogenosomes lack a genome, but some like that of the anaerobic ciliate Nyctotherus ovalis, have retained a rudimentary genome.Hydrogenosome http://purl.uniprot.org/locations/145The membrane surrounding the hydrogenosome, a redox organelle found in anaerobic unicellular eukaryotes.Hydrogenosome membrane The peroxisome is a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions. Contains mainly peroxidases, several other oxidases and catalase. The catalase regulates the contents of the produced toxic hydrogen peroxide thus protecting the cell. Beta-oxidation of fatty acids is another major function of peroxisomes. In plants and fungi this degradation occurs only in this cellular compartment.Peroxisome http://purl.uniprot.org/locations/204The membrane surrounding the the glycosome, a specialized peroxisome found in all members of the protist order Kinetoplastida examined.Glycosome membraneThe membrane surrounding the glyoxysome, a plant peroxisome, especially found in germinating seeds, involved in the breakdown and conversion of fatty acids to acetyl-CoA for the glyoxylate bypass.Glyoxysome membraneThe membrane surrounding a peroxysome.Peroxisome membrane The melanosome is a melanin-containing organelle found in melanocytes and melanophores. Fish and amphibians possess specialized cells, called melanophores, which contain hundreds of melanin-filled pigment granules, termed melanosomes. The sole function of these cells is pigment aggregation in the center of the cell or dispersion throughout the cytoplasm. This alternative transport of pigment allows the animal to effect color changes important for camouflage and social interactions. Melanophores transport their pigment in response to extracellular cues: neurotransmitters in the case of fish and hormonal stimuli in the case of frogs. In both cases, melanosome dispersion is induced by elevation of intracellular cAMP levels, while aggregation is triggered by depression of cAMP. The regulatory mechanisms downstream of these second-messengers are poorly understood. Mammalian melanocytes also produce melanosomes but, unlike melanophores, pigment in these cells is transported to the cell periphery for subsequent exocytosis to surrounding epithelial cells.Melanosome http://purl.uniprot.org/locations/161The membrane surrounding a melanosome.Melanosome membrane The organellar chromatophore is the photosynthetic inclusion found in Paulinella species, which are photosynthetic thecate amoeba. It probably derives from a different endosymbiotic event than that which led to all other plastids. Houses the machinery necessary for photosynthesis and CO(2) fixation and may also be able to make a few amino acids, some fatty acids and a few cofactors. They are surrounded by 2 membranes, between which is found a residual peptidoglycan wall, and contain thylakoids.Organellar chromatophore http://purl.uniprot.org/locations/351One of the membranes of an organellar chromatophore. This term is used when it is not known with which membrane (outer membrane, inner membrane or thylakoid) a protein is associated. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore membraneThe organellar chromatophore thylakoid membrane is an internal system of interconnected membranes that house the complexes which carry out the light reactions of photosynthesis. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore thylakoid membraneThe organellar chromatophore inner membrane is the membrane which separates the chromatophore stroma from the intermembrane space. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore inner membraneThe organellar chromatophore outer membrane is the organellar chromatophore membrane facing the cytoplasm. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore outer membrane A contractile vacuole (CV) complex is a membrane-bound osmoregulatory organelle of fresh water and soil amoebae and protozoa which segregates excess cytosolic water, acquired osmotically, and expel it to the cell exterior, so that the cytosolic osmolarity is kept constant under a given osmotic condition. Depending on the organism, the CV complex (CVC) shows different degrees of specialization of its tubular and vesicular elements. In the most elaborate CVCs of certain ciliates, e.g. Paramecium, a central vacuole, the contractile vacuole or cisterna, is surrounded by radially oriented ampullae or radial arms. These ampullae are connected to a network of channels. Excess cytosolic water, acquired osmotically, is segregated by the radial arms and enters the vacuole, so that the vacuole swells (the fluid-filling phase). The vacuole then rounds (the rounding phase) and the radial arms sever from the vacuole. The vacuole membrane then fuses with the plasma membrane at the pore region and the pore opens. The vacuole shrinks as its fluid is discharged through the pore (the fluid-discharging phase). The pore closes when the fluid has been discharged. The radial arms then reattach to the vacuole, so that the vacuole swells again as the fluid enters from the arms (the next fluid-filling phase).Contractile vacuole http://purl.uniprot.org/locations/73The membrane surrounding a contractile vacuole. A contractile vacuole (CV) complex is a membrane-bound osmoregulatory organelle of fresh water and soil amoebae and protozoa which segregates excess cytosolic water, acquired osmotically, and expel it to the cell exterior, so that the cytosolic osmolarity is kept constant under a given osmotic condition.Contractile vacuole membrane The autophagosome is a double membrane vesicle involved in the degradation of long-lived proteins, unnecessary or damaged organelles as well as other cellular constituents such as lipids or carbohydrates. Crescent-shape isolation membranes or phagophores can sequester cytoplasm and organelles giving rise to autophagosomes. The outer membrane of the autophagosomes then fuse with vacuoles and/or lysosomes and the inner membrane vesicles (termed autophagic bodies) are released into the vacuole/lysosome lumen. These vesicles are then lysed and the contents are degraded by resident hydrolases.Autophagosome http://purl.uniprot.org/locations/23The membrane surrounding the autophagosome.Autophagosome membrane COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle http://purl.uniprot.org/locations/75The membrane surrounding a COPI-coated vesicle. COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle membrane COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle http://purl.uniprot.org/locations/77The membrane surrounding a COPII-coated vesicle. COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle membrane The ER-Golgi intermediate compartment is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites. The ERGIC mediates transport between the endoplasmic reticulum and the Golgi and is the first anterograde/retrograde sorting station in the secretory pathway. ERGIC has not been observed in yeast and plants.Endoplasmic reticulum-Golgi intermediate compartment http://purl.uniprot.org/locations/98The membrane surrounding the ER-Golgi intermediate compartment, which is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites.Endoplasmic reticulum-Golgi intermediate compartment membrane Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface. They also receive newly synthesised proteins destined for vacuolar/lysosomal compartments. In certain cell types, endosomal multivesicular bodies may fuse with the cell surface in an exocytic manner. These released vesicles are called exosomes.Endosome Late endosomes are pleiomorphic with cisternal, tubular and multivesicular regions. They are found in juxtanuclear regions and concentrated at the microtubule organizing center. They are an important sorting station in the endocytic pathway. Recycling to the plasma membrane and to the Golgi occurs in late endosomes. More acidic than early endosomes they are also loaded more slowly in a range of 4 to 30 minutes depending on the cell type. They can be distinguished from lysosome for their enrichment in M6PR.Late endosome http://purl.uniprot.org/locations/152The membrane surrounding the late endosomes.Late endosome membrane Early endosomes form a tubulovesicular network spread throughout the cortical cytoplasm of the cell. Early endosomes are the primary sorting station in the endocytic pathway from which endocytosed molecules can be recycled back to the cell membrane or targeted to degradation in the lysosomes. Loaded by endocytosed molecules in 1 to 4 minutes, their acidic luminal pH around 6.0 allows ligand release from recycling receptors.Early endosome http://purl.uniprot.org/locations/94The membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membrane The multivesicular bodies are a type of late endosome containing internal vesicles formed following the inward budding of the outer endosomal membrane. The contents of the MVBs are then released into the lysosome lumen. The proteins found in the limiting membrane of MVBs are recycled to other compartments.Multivesicular body http://purl.uniprot.org/locations/174The membrane surrounding the multivesicular bodies.Multivesicular body membrane Clathrin coated vesicles (CCVs) mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle http://purl.uniprot.org/locations/70The membrane surrounding a clathrin-coated vesicle (CCV). CCVs mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle membrane http://purl.uniprot.org/locations/101The membrane surrounding the endosome. Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface.Endosome membraneThe membrane surrounding the late endosomes.Late endosome membraneThe membrane surrounding the recycling endosomes.Recycling endosome membraneThe membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membraneThe membrane surrounding the multivesicular bodies.Multivesicular body membrane The caveola is a small (apparently) uncoated pit mostly found in the cell membrane of many highly differentiated mammalian cells, such as adipocytes, endothelial cells and muscle cells. These flask-shaped invaginations are defined by the presence of caveolins and contains a subset of lipid-raft components, including cholesterol and sphingolipids. Caveolae each comprise a caveolar bulb with a diameter of 60-80 nm, connected to an opening of fairly constant diameter. Caveolae might exists as single pits or can form a cluster of caveolae with non-caveolar membrane between the pits. In many tissues, and particularly in adipocytes, multiple caveolae are arranged around a central vacuolar domain. In developing muscle fibres, multiple caveolae are connected by a single neck to the cell membrane, producing large chains of interconnected caveolae. Another structural feature of caveolae in certain endothelia is the presence of a stomatal diaphragm, which consists of a central density and radial spikes, in the neck of the caveolae. Mature caveolae might be assembled in the Golgi apparatus. Caveolae can flatten out into the cell membrane, thereby loosing their caveolar identity.Caveola http://purl.uniprot.org/locations/35 Coated pits are regions of the donor membrane where the assembly of the vesicle coat take place. The coat assembles from soluble protomers such as coat protein complex-I and coat protein complex-II. The components of the coat often define the intracellular sorting station, and contribute to both membrane deformation and local movement of the resulting transport intermediate following scission. During the first steps of the vesicle-mediated membrane transport, coated pits are internalized to form coated vesicles which transport proteins between distinct membrane-bound organelles.Coated pit Coated pits are regions of the cell membrane specialized in receptor-mediated endocytosis. Their cytoplasmic surface is coated with a bristlelike structure made of clathrin. During the first steps of endocytosis, clathrin-coated pits are internalized to form clathrin-coated vesicles which transport proteins from organelle to organelle.Clathrin-coated pit http://purl.uniprot.org/locations/69 http://purl.uniprot.org/locations/72 The lysosome is a membrane-limited organelle present in all eukaryotic cells, which contains a large number of hydrolytic enzymes that are used for degrading almost any kind of cellular constituent, including entire organelles. The mechanisms responsible for delivering cytoplasmic cargo to the lysosome/vacuole are known collectively as autophagy and play an important role in the maintenance of homeostasis.Lysosome http://purl.uniprot.org/locations/158The cytolytic granule membrane is the membrane surrounding a cytolytic granule.Cytolytic granule membraneThe membrane surrounding a lysosome.Lysosome membrane Cup-shaped invaginations of the cell membrane that subsequently close at their distal margins to form phagosomes during phagocytosis. By progression of its rim along the particle surface, this phagocytic cup envelops and eventually encloses the particle by separation of the phagosome membrane from the cell membrane. Filamentous actin accumulates between the outer and inner leaflet of the cup membrane and is most strongly enriched at the rim of the cup, the site of its protrusion.Phagocytic cup http://purl.uniprot.org/locations/473 The phagosome is a phagocytic cell-specific compartment. These large endocytic membrane-bound vesicles form upon ingestion by the cell of extracellular materials.Phagosome http://purl.uniprot.org/locations/206The membrane surrounding a phagosome.Phagosome membrane Focal adhesions are sites of tightest adhesion made to the underlying extracellular matrix by cells in culture. They serve a structural role, linking the ECM on the outside to the actin cytoskeleton on the inside. In addition, they are sites of signal transduction, initiating signaling pathways in response to adhesion. Focal adhesions are formed around a transmembrane core of an alpha-beta integrin heterodimer, which binds to a component of the extracellular matrix on its extracellular region, constitutes the site of anchorage of the actin cytoskeleton to the cytoplasmic side of the membrane, and mediates various intracellular signaling pathways.Focal adhesion http://purl.uniprot.org/locations/118 The lipid droplet is a dynamic cytoplasmic organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. Lipid droplets may play a role in lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.Lipid droplet http://purl.uniprot.org/locations/154 A chromaffin granule is a specialized secretory vesicle characteristic of chromaffin cells.Chromaffin granule http://purl.uniprot.org/locations/61The chromaffin granule membrane is the membrane surrounding a chromaffin granule, a specialized secretory vesicle characteristic of chromaffin cells.Chromaffin granule membrane Protein found in or associated with cytoplasmic granules.Cytoplasmic granule http://purl.uniprot.org/locations/281The membrane surrounding a cytoplasmic granule.Cytoplasmic granule membrane Philippe Le Mercier Animal cell

Animal Egg Cell: Peullucida

{{< sbp Egg_Cell highlight=pellucida >}}
Protein located outside the cell membrane(s).Secreted The extracellular space is the space outside of the cell membrane but part of a multicellular organism. The term is typically used for a secreted protein that remains associated with the cell, e.g. as part of the extracellular matrix. It is not used for a protein that is secreted into the blood stream (or other body fluids) of eukaryotic, multicellular organisms, such as insulin or fibroblast growth factors.Extracellular space http://purl.uniprot.org/locations/112 The extracellular matrix (ECM) is a vague term used to refer to all the material surrounding cells in a multicellular organism, except circulating fluids such as blood or lymph. In some cases, the ECM accounts for more of the organism's bulk than its cells. In plants, arthropods and fungi the ECM is primarily composed of nonliving material such as cellulose or chitin. In vertebrates the ECM consists of a complex network including the basement membrane, collage, elastin, proteoglycans and hyaluronan.Extracellular matrix Zona pellucida is a specialized extracellular matrix that surrounds the plasma membrane of mammalian oocytes. It is required for successful fertilization. Zona pellucida allows species-specific fertilization, prevents polyspermy, and enables acrosomal reaction for the successful adhesion and penetration of the sperm cell.Zona pellucida http://purl.uniprot.org/locations/540 http://purl.uniprot.org/locations/111 http://purl.uniprot.org/locations/243 The cytoplasm is the content of a cell within the plasma membrane and, in eukaryotics cells, surrounding the nucleus. This three-dimensional, jelly-like lattice interconnects and supports the other solid structures. The cytosol (the soluble portion of the cytoplasm outside the organelles) is mostly composed of water and many low molecular weight compounds. In eukaryotes, the cytoplasm also contains a network of cytoplasmic filaments (cytoskeleton).Cytoplasm The cytosol is the unstructured aqueous phase of the cytoplasm excluding organelles, membranes, and insoluble cytoskeletal components.Cytosol http://purl.uniprot.org/locations/91 http://purl.uniprot.org/locations/86 The cell cortex is the cytoplasmic region under the cell membrane.Cell cortex http://purl.uniprot.org/locations/138 The perinuclear region is the cytoplasmic region just around the nucleus.Perinuclear region http://purl.uniprot.org/locations/198 The cytoskeleton is a dynamic three-dimensional filamentous structure in the cytoplasm. Its roles include maintenance of cell shape, cell movement (in eukaryotes), cytokinesis, and the organization of organelles or organelle-like structures within the cell. The cytoskeleton includes microfilaments (actin-like proteins), microtubules (tubulin-like proteins), the intermediate filaments (mostly in eukaryotes) and the MinD-ParA proteins, which appear to be unique to prokaryotes.Cytoskeleton Stress fibers are contractile actomyosin bundles found in non-muscle cells, in eukaryotes, mostly in animals. They are composed of bundles of 10 to 30 actin filaments (microfilaments), crosslinked by alpha-actinin, and non-muscle myosin. They are often anchored to focal adhesions, that connect the extracellular matrix to the actin cytoskeleton. Stress fibers play an essential role in cell contractility, governing cell morphology, adhesion, and migration. In non-motile cells, stress fibers are usually thick and relatively stable. By contrast, highly motile cells typically contain fewer, thinner and more dynamic stress fibers. Stress fibers can be divided into at least 4 different categories : dorsal and ventral stress fibers, transverse arcs and the perinuclear actin cap.Stress fiber http://purl.uniprot.org/locations/501 The microtubule organizing center (MTOC) is an intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules.Microtubule organizing center The centrosome is a microtubule organizing center (MTOC) responsible for the nucleation and organisation of microtubules. It is composed of two orthogonally arranged centrioles, each one having a barrel shaped microtubule structure, and their surrounding pericentriolar material (PCM).Centrosome The centriole is a barrel-shaped microtubule-based structure. A pair of centrioles, embedded in the so-called pericentriolar material, constitute the centrosome, a microtubule organizing center of an eukaryotic cell. Centrioles are barrel-shaped microtubule-based structures organized in a 9-fold radial symmetry. Centriolar microtubule arrays usually consist of triplet microtubules, although doublets or singlets are present in some species. Centrioles are structurally related to (and often interconvertible with) basal bodies, the organelles required for the assembly of a cilium or flagellum.Centriole http://purl.uniprot.org/locations/46 Centriolar satellites are nonmembranous, electron-dense and spherical cytoplasmic granules of about 70-100 nm in diameter, occurring around centrosomes in most vertebrate cell types. They contain a number of centrosomal proteins. Centriolar satellites have the ability to move along microtubules, toward their minus ends, i.e. toward centrosomes. Their number increase during interphase and decrease during mitosis.Centriolar satellite http://purl.uniprot.org/locations/485 http://purl.uniprot.org/locations/48 http://purl.uniprot.org/locations/484 http://purl.uniprot.org/locations/90 The cell membrane is the selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the cell inner membrane in prokaryotes with 2 membranes.Cell membrane http://purl.uniprot.org/locations/39 The outermost side of the cell.Cell surface http://purl.uniprot.org/locations/310 The nucleus is the most obvious organelle in any eukaryotic cell. It is a membrane-bound organelle surrounded by double membranes which contains most of the cell's genetic material. It communicates with the surrounding cytosol via numerous nuclear pores.Nucleus The nucleoplasm is a highly viscous liquid contained within the nucleus that surrounds the chromosomes and other subnuclear organelles. A network of fibers known as the nuclear matrix can also be found in the nucleoplasm.Nucleoplasm http://purl.uniprot.org/locations/190 The membrane surrounding the nucleus. This term is used when it is not known if the protein is found in or associated with the inner or outer nuclear membrane.Nucleus membrane http://purl.uniprot.org/locations/182 The nucleolus is a non-membrane bound nuclear compartment found in eukaryotic cells which is the site of ribosome biogenesis. The interphase nucleolus is organized around the tandemly repeated genes for preribosomal RNA (rRNA). It is composed of at least 2 sub-compartments: the dense fibrillar component (DFC, also called pars fibrosa) and the granular component (GC or pars granulosa). The DFC contains newly synthesized preribosomal RNA and a collection of proteins; the GC is made up of nearly completed preribosomal particles destined for the cytoplasm. In most metazoans, but generally not in lower eukaryotes, a third component, the fibrillar center (FC), can be seen. Plant and animal nuclei can contain more than one nucleolus.Nucleolus http://purl.uniprot.org/locations/188 Nuclear body is a collective term for several nuclear, extra-nucleolar, non-membrane-bound sub-compartments, including, but not limited to Cajal bodies, Gemini of Cajal bodies (gems), nuclear speckles and PML bodies. Nuclear bodies are visible as distinct spots in the nucleoplasm. They can vary in number and size depending on the cell line and the type of nuclear body.Nuclear body Gems are nuclear bodies, often found paired or juxtaposed to Cajal bodies, called gems for "gemini of CBs". It is not clear if Cajal bodes and gems are distinct nuclear bodies or if they should be considered as two manifestations of the same structure.Gem http://purl.uniprot.org/locations/127 The nuclear Cajal bodies (CBs) are small subnuclear membraneless organelles present either free in the nucleoplasm and/or physically associated to specific regions of chromatin. CBs contain newly assembled small nuclear ribonucleoproteins (snRNPs) and small nucleolar ribonucleoproteins (snoRNPs) particles, which are involved in pre-mRNA splicing and in ribosomal RNA processing, respectively. Mammalian nucleus in interphase, show 2-6 CBs, as irregular, punctuate structures, which vary in size and shape and which are often juxtaposed to nucleoli. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called coiled body. Structures similar to CBs have been identified in the amphibian oocyte nucleus (called sphere organelles) and in insect (called endobodies). CBs are motile and dynamic structures. Both their protein and RNA-protein components can cycle continuously between CBs and other nuclear locations depending on the transcriptional state of the cell.Cajal body http://purl.uniprot.org/locations/31 The PML bodies are dynamic nuclear protein aggregates interspersed between chromatin. These punctate nuclear structures are call PML bodies because the PML gene is essential for their formation. These discrete nuclear foci, 0.2-1.0 micrometer wide, are present in most mammalian cell nuclei and typically number 1 to 30 bodies per nucleus, depending on the cell type, cell-cycle phase and differentiation stage. Recent evidence implies that, although they appear to be uniform, PML-NBs are structurally and functionally heterogeneous and are dynamic structures.PML body http://purl.uniprot.org/locations/465 The nuclear speckles are small subnuclear membraneless organelles or structures, also called the splicing factor (SF) compartments that correspond to nuclear domains located in interchromatin regions of the nucleoplasm of mammalian cells. Protein found in speckles serves as a reservoir of factors that participate in transcription and pre-mRNA processing. Speckles appear, at the immunofluorescence-microscope level, as irregular, punctuate structures, which vary in size and shape. Usually 25-50 speckles are observed per interphase mammalian nucleus. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called interchromatin granules clusters (IGCs). Speckles are dynamic structures. Both their protein and RNA-protein components can cycle continuously between speckles and other nuclear locations depending on the transcriptional state of the cell. Structures similar to nuclear speckles have been identified in the amphibian oocyte nucleus (called B snurposomes) and in Drosophila melanogaster embryos, but not in yeast.Nucleus speckle http://purl.uniprot.org/locations/186 http://purl.uniprot.org/locations/494 The nuclear lamina is a meshwork of intermediate filament proteins called lamins and lamin-binding proteins that are embedded in the inner nuclear membrane.Nucleus lamina http://purl.uniprot.org/locations/180 http://purl.uniprot.org/locations/191The inner membrane of the nucleus is the membrane which separates the nuclear matrix from the intermembrane space. In mammals, the inner nuclear membrane is associated with heterochromatin and the nuclear lamina.Nucleus inner membraneThe outer membrane of the nucleus is the membrane facing the cytoplasm. In mammals, the outer nuclear membrane is continuous in many places with the rough endoplasmic reticulum and is dotted with ribosomes.Nucleus outer membrane The mitochondrion is a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. The size and coding capacity of the mitochondrial DNA varies considerably in different organisms, and encodes rRNAs, tRNAs and essential mitochondrial proteins.Mitochondrion http://purl.uniprot.org/locations/173The inner membrane of a mitochondrion is the membrane which separates the mitochondrial matrix from the intermembrane space.Mitochondrion inner membraneThe membrane surrounding a mitochondrion. This term is used when it is not known if the protein is found in or associated with the inner or outer mitochondrial membrane.Mitochondrion membraneThe outer membrane of a mitochondrion is the mitochondrial membrane facing the cytoplasm.Mitochondrion outer membrane The endoplasmic reticulum (ER) is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products. The membrane is a continuation of the outer nuclear membrane, it encloses the cytosol cisternal spaces (or internal lumen), which are continuous with the nuclear periplasmic space. The ER sustains many general functions, including protein synthesis, protein modification, protein folding, insertion of membrane proteins, sequestration of calcium, production of phospholipids and steroids and transport of proteins destined for membranes and secretion.Endoplasmic reticulum The smooth endoplasmic reticulum (SER) is the portion of the ER which is free of ribosomes.Smooth endoplasmic reticulum http://purl.uniprot.org/locations/248The membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membrane The rough endoplasmic reticulum (RER) is the portion of the ER which is covered with ribosomes.Rough endoplasmic reticulum http://purl.uniprot.org/locations/235The membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane http://purl.uniprot.org/locations/95The membrane surrounding the endoplasmic reticulum (ER). The endoplasmic reticulum is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products.Endoplasmic reticulum membraneThe membrane surrounding the microsome.Microsome membraneThe membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membraneThe membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane The Golgi apparatus is a series of flattened, cisternal membranes and similar vesicles usually arranged in close apposition to each other to form stacks. In mammalian cells, the Golgi apparatus is juxtanuclear, often pericentriolar. The stacks are connected laterally by tubules to create a perinuclear ribbon structure, the 'Golgi ribbon'. In plants and lower animal cells, the Golgi exists as many copies of discrete stacks dispersed throughout the cytoplasm. The Golgi is a polarized structure with, in most higher eukaryotic cells, a cis-face associated with a tubular reticular network of membranes facing the endoplasmic reticulum, the cis-Golgi network (CGN), a medial area of disk-shaped flattened cisternae, and a trans-face associated with another tubular reticular membrane network, the trans-Golgi network (TGN) directed toward the plasma membrane and compartments of the endocytic pathway. The Golgi apparatus receives the entire output of de novo synthesized polypeptides from the ER, and functions to posttranslationally process and sort them within vesicles destined to their proper final destination (e.g. plasma membrane, endosomes, lysosomes).Golgi apparatus The trans-Golgi network is a highly dynamic series of interconnected tubules and vesicles at the trans face of the Golgi stack. The trans-Golgi network functions in the processing and sorting of glycoproteins and glycolipids at the interface of the biosynthetic and endosomal pathways. The generation and maintenance of apical and basolateral membranes rely on sorting events that occur in the TGN.trans-Golgi network http://purl.uniprot.org/locations/266The membrane surrounding the trans-Golgi network.trans-Golgi network membrane The Golgi stack consist of a series of flattened curved and parallel series saccules, called cisternae or dictyosomes, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.Golgi stack http://purl.uniprot.org/locations/135The membrane surrounding the Golgi stack.Golgi stack membrane The cis-Golgi network is an extensive tubulovesicular network bound to the cis face of the Golgi stack and which function is to receive process the biosynthetic output from the ER.cis-Golgi network http://purl.uniprot.org/locations/67The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membrane http://purl.uniprot.org/locations/132The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membraneThe membrane surrounding the Golgi apparatus.Golgi apparatus membraneThe membrane surrounding the Golgi stack.Golgi stack membraneThe membrane surrounding the trans-Golgi network.trans-Golgi network membrane The peroxisome is a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions. Contains mainly peroxidases, several other oxidases and catalase. The catalase regulates the contents of the produced toxic hydrogen peroxide thus protecting the cell. Beta-oxidation of fatty acids is another major function of peroxisomes. In plants and fungi this degradation occurs only in this cellular compartment.Peroxisome http://purl.uniprot.org/locations/204The membrane surrounding the the glycosome, a specialized peroxisome found in all members of the protist order Kinetoplastida examined.Glycosome membraneThe membrane surrounding the glyoxysome, a plant peroxisome, especially found in germinating seeds, involved in the breakdown and conversion of fatty acids to acetyl-CoA for the glyoxylate bypass.Glyoxysome membraneThe membrane surrounding a peroxysome.Peroxisome membrane The melanosome is a melanin-containing organelle found in melanocytes and melanophores. Fish and amphibians possess specialized cells, called melanophores, which contain hundreds of melanin-filled pigment granules, termed melanosomes. The sole function of these cells is pigment aggregation in the center of the cell or dispersion throughout the cytoplasm. This alternative transport of pigment allows the animal to effect color changes important for camouflage and social interactions. Melanophores transport their pigment in response to extracellular cues: neurotransmitters in the case of fish and hormonal stimuli in the case of frogs. In both cases, melanosome dispersion is induced by elevation of intracellular cAMP levels, while aggregation is triggered by depression of cAMP. The regulatory mechanisms downstream of these second-messengers are poorly understood. Mammalian melanocytes also produce melanosomes but, unlike melanophores, pigment in these cells is transported to the cell periphery for subsequent exocytosis to surrounding epithelial cells.Melanosome http://purl.uniprot.org/locations/161The membrane surrounding a melanosome.Melanosome membrane The autophagosome is a double membrane vesicle involved in the degradation of long-lived proteins, unnecessary or damaged organelles as well as other cellular constituents such as lipids or carbohydrates. Crescent-shape isolation membranes or phagophores can sequester cytoplasm and organelles giving rise to autophagosomes. The outer membrane of the autophagosomes then fuse with vacuoles and/or lysosomes and the inner membrane vesicles (termed autophagic bodies) are released into the vacuole/lysosome lumen. These vesicles are then lysed and the contents are degraded by resident hydrolases.Autophagosome http://purl.uniprot.org/locations/23The membrane surrounding the autophagosome.Autophagosome membrane COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle http://purl.uniprot.org/locations/75The membrane surrounding a COPI-coated vesicle. COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle membrane COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle http://purl.uniprot.org/locations/77The membrane surrounding a COPII-coated vesicle. COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle membrane The ER-Golgi intermediate compartment is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites. The ERGIC mediates transport between the endoplasmic reticulum and the Golgi and is the first anterograde/retrograde sorting station in the secretory pathway. ERGIC has not been observed in yeast and plants.Endoplasmic reticulum-Golgi intermediate compartment http://purl.uniprot.org/locations/98The membrane surrounding the ER-Golgi intermediate compartment, which is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites.Endoplasmic reticulum-Golgi intermediate compartment membrane Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface. They also receive newly synthesised proteins destined for vacuolar/lysosomal compartments. In certain cell types, endosomal multivesicular bodies may fuse with the cell surface in an exocytic manner. These released vesicles are called exosomes.Endosome Late endosomes are pleiomorphic with cisternal, tubular and multivesicular regions. They are found in juxtanuclear regions and concentrated at the microtubule organizing center. They are an important sorting station in the endocytic pathway. Recycling to the plasma membrane and to the Golgi occurs in late endosomes. More acidic than early endosomes they are also loaded more slowly in a range of 4 to 30 minutes depending on the cell type. They can be distinguished from lysosome for their enrichment in M6PR.Late endosome http://purl.uniprot.org/locations/152The membrane surrounding the late endosomes.Late endosome membrane Early endosomes form a tubulovesicular network spread throughout the cortical cytoplasm of the cell. Early endosomes are the primary sorting station in the endocytic pathway from which endocytosed molecules can be recycled back to the cell membrane or targeted to degradation in the lysosomes. Loaded by endocytosed molecules in 1 to 4 minutes, their acidic luminal pH around 6.0 allows ligand release from recycling receptors.Early endosome http://purl.uniprot.org/locations/94The membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membrane The multivesicular bodies are a type of late endosome containing internal vesicles formed following the inward budding of the outer endosomal membrane. The contents of the MVBs are then released into the lysosome lumen. The proteins found in the limiting membrane of MVBs are recycled to other compartments.Multivesicular body http://purl.uniprot.org/locations/174The membrane surrounding the multivesicular bodies.Multivesicular body membrane Clathrin coated vesicles (CCVs) mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle http://purl.uniprot.org/locations/70The membrane surrounding a clathrin-coated vesicle (CCV). CCVs mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle membrane Coated pits are regions of the cell membrane specialized in receptor-mediated endocytosis. Their cytoplasmic surface is coated with a bristlelike structure made of clathrin. During the first steps of endocytosis, clathrin-coated pits are internalized to form clathrin-coated vesicles which transport proteins from organelle to organelle.Clathrin-coated pit http://purl.uniprot.org/locations/69 The caveola is a small (apparently) uncoated pit mostly found in the cell membrane of many highly differentiated mammalian cells, such as adipocytes, endothelial cells and muscle cells. These flask-shaped invaginations are defined by the presence of caveolins and contains a subset of lipid-raft components, including cholesterol and sphingolipids. Caveolae each comprise a caveolar bulb with a diameter of 60-80 nm, connected to an opening of fairly constant diameter. Caveolae might exists as single pits or can form a cluster of caveolae with non-caveolar membrane between the pits. In many tissues, and particularly in adipocytes, multiple caveolae are arranged around a central vacuolar domain. In developing muscle fibres, multiple caveolae are connected by a single neck to the cell membrane, producing large chains of interconnected caveolae. Another structural feature of caveolae in certain endothelia is the presence of a stomatal diaphragm, which consists of a central density and radial spikes, in the neck of the caveolae. Mature caveolae might be assembled in the Golgi apparatus. Caveolae can flatten out into the cell membrane, thereby loosing their caveolar identity.Caveola http://purl.uniprot.org/locations/35 http://purl.uniprot.org/locations/101The membrane surrounding the endosome. Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface.Endosome membraneThe membrane surrounding the late endosomes.Late endosome membraneThe membrane surrounding the recycling endosomes.Recycling endosome membraneThe membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membraneThe membrane surrounding the multivesicular bodies.Multivesicular body membrane The lysosome is a membrane-limited organelle present in all eukaryotic cells, which contains a large number of hydrolytic enzymes that are used for degrading almost any kind of cellular constituent, including entire organelles. The mechanisms responsible for delivering cytoplasmic cargo to the lysosome/vacuole are known collectively as autophagy and play an important role in the maintenance of homeostasis.Lysosome http://purl.uniprot.org/locations/158The cytolytic granule membrane is the membrane surrounding a cytolytic granule.Cytolytic granule membraneThe membrane surrounding a lysosome.Lysosome membrane The phagosome is a phagocytic cell-specific compartment. These large endocytic membrane-bound vesicles form upon ingestion by the cell of extracellular materials.Phagosome http://purl.uniprot.org/locations/206The membrane surrounding a phagosome.Phagosome membrane The lipid droplet is a dynamic cytoplasmic organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. Lipid droplets may play a role in lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.Lipid droplet http://purl.uniprot.org/locations/154 A chromaffin granule is a specialized secretory vesicle characteristic of chromaffin cells.Chromaffin granule http://purl.uniprot.org/locations/61The chromaffin granule membrane is the membrane surrounding a chromaffin granule, a specialized secretory vesicle characteristic of chromaffin cells.Chromaffin granule membrane Protein found in or associated with cytoplasmic granules.Cytoplasmic granule http://purl.uniprot.org/locations/281The membrane surrounding a cytoplasmic granule.Cytoplasmic granule membrane Cortical granules are secretory organelles located under the cell membrane of unfertilized oocytes. Following fertilization, cortical granules fuse with the oocyte's cell membrane and release their contents into the extracellular matrix. This exocytosis, known as the cortical reaction, is involved in the prevention of polyspermy. Cortical granules are found in all mammals and many other vertebrates, as well as some invertebrates.Cortical granule http://purl.uniprot.org/locations/541 Philippe Le Mercier Animal egg cell

Eukaryota Cell Cytosol: Spore

{{< sbp Eukaryota_cells highlight=spore >}}
Protein located outside the cell membrane(s).Secreted The extracellular matrix (ECM) is a vague term used to refer to all the material surrounding cells in a multicellular organism, except circulating fluids such as blood or lymph. In some cases, the ECM accounts for more of the organism's bulk than its cells. In plants, arthropods and fungi the ECM is primarily composed of nonliving material such as cellulose or chitin. In vertebrates the ECM consists of a complex network including the basement membrane, collage, elastin, proteoglycans and hyaluronan.Extracellular matrix http://purl.uniprot.org/locations/111 Exosomes are 30-120 nm microvesicles of endocytic origin secreted by most cell types and found in abundance in body fluids, including blood, saliva, urine, and breast milk. They contain various molecular constituents of their cell of origin, including proteins and nucleic acids, and carry this cargo between diverse locations in the body. These microvesicles form by budding into the lumen of the multivesicular bodies (MVBs) and are released to extracellular fluids by fusion of MVBs with the plasma membrane.Extracellular exosome http://purl.uniprot.org/locations/466 http://purl.uniprot.org/locations/243 The cytoplasm is the content of a cell within the plasma membrane and, in eukaryotics cells, surrounding the nucleus. This three-dimensional, jelly-like lattice interconnects and supports the other solid structures. The cytosol (the soluble portion of the cytoplasm outside the organelles) is mostly composed of water and many low molecular weight compounds. In eukaryotes, the cytoplasm also contains a network of cytoplasmic filaments (cytoskeleton).Cytoplasm The cytosol is the unstructured aqueous phase of the cytoplasm excluding organelles, membranes, and insoluble cytoskeletal components.Cytosol http://purl.uniprot.org/locations/91 http://purl.uniprot.org/locations/86 The cell cortex is the cytoplasmic region under the cell membrane.Cell cortex http://purl.uniprot.org/locations/138 The region at either end of the longest axis of a cylindrical or elongated cell, where polarized growth may occur.Cell tip http://purl.uniprot.org/locations/456 The perinuclear region is the cytoplasmic region just around the nucleus.Perinuclear region http://purl.uniprot.org/locations/198 The cytoskeleton is a dynamic three-dimensional filamentous structure in the cytoplasm. Its roles include maintenance of cell shape, cell movement (in eukaryotes), cytokinesis, and the organization of organelles or organelle-like structures within the cell. The cytoskeleton includes microfilaments (actin-like proteins), microtubules (tubulin-like proteins), the intermediate filaments (mostly in eukaryotes) and the MinD-ParA proteins, which appear to be unique to prokaryotes.Cytoskeleton The microtubule organizing center (MTOC) is an intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules.Microtubule organizing center The centrosome is a microtubule organizing center (MTOC) responsible for the nucleation and organisation of microtubules. It is composed of two orthogonally arranged centrioles, each one having a barrel shaped microtubule structure, and their surrounding pericentriolar material (PCM).Centrosome The centriole is a barrel-shaped microtubule-based structure. A pair of centrioles, embedded in the so-called pericentriolar material, constitute the centrosome, a microtubule organizing center of an eukaryotic cell. Centrioles are barrel-shaped microtubule-based structures organized in a 9-fold radial symmetry. Centriolar microtubule arrays usually consist of triplet microtubules, although doublets or singlets are present in some species. Centrioles are structurally related to (and often interconvertible with) basal bodies, the organelles required for the assembly of a cilium or flagellum.Centriole http://purl.uniprot.org/locations/46 Centriolar satellites are nonmembranous, electron-dense and spherical cytoplasmic granules of about 70-100 nm in diameter, occurring around centrosomes in most vertebrate cell types. They contain a number of centrosomal proteins. Centriolar satellites have the ability to move along microtubules, toward their minus ends, i.e. toward centrosomes. Their number increase during interphase and decrease during mitosis.Centriolar satellite http://purl.uniprot.org/locations/485 http://purl.uniprot.org/locations/48 http://purl.uniprot.org/locations/484 http://purl.uniprot.org/locations/90 The cell membrane is the selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the cell inner membrane in prokaryotes with 2 membranes.Cell membrane http://purl.uniprot.org/locations/39 The nucleus is the most obvious organelle in any eukaryotic cell. It is a membrane-bound organelle surrounded by double membranes which contains most of the cell's genetic material. It communicates with the surrounding cytosol via numerous nuclear pores.Nucleus The nucleoplasm is a highly viscous liquid contained within the nucleus that surrounds the chromosomes and other subnuclear organelles. A network of fibers known as the nuclear matrix can also be found in the nucleoplasm.Nucleoplasm http://purl.uniprot.org/locations/190 The membrane surrounding the nucleus. This term is used when it is not known if the protein is found in or associated with the inner or outer nuclear membrane.Nucleus membrane http://purl.uniprot.org/locations/182 Nuclear body is a collective term for several nuclear, extra-nucleolar, non-membrane-bound sub-compartments, including, but not limited to Cajal bodies, Gemini of Cajal bodies (gems), nuclear speckles and PML bodies. Nuclear bodies are visible as distinct spots in the nucleoplasm. They can vary in number and size depending on the cell line and the type of nuclear body.Nuclear body Gems are nuclear bodies, often found paired or juxtaposed to Cajal bodies, called gems for "gemini of CBs". It is not clear if Cajal bodes and gems are distinct nuclear bodies or if they should be considered as two manifestations of the same structure.Gem http://purl.uniprot.org/locations/127 The nuclear Cajal bodies (CBs) are small subnuclear membraneless organelles present either free in the nucleoplasm and/or physically associated to specific regions of chromatin. CBs contain newly assembled small nuclear ribonucleoproteins (snRNPs) and small nucleolar ribonucleoproteins (snoRNPs) particles, which are involved in pre-mRNA splicing and in ribosomal RNA processing, respectively. Mammalian nucleus in interphase, show 2-6 CBs, as irregular, punctuate structures, which vary in size and shape and which are often juxtaposed to nucleoli. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called coiled body. Structures similar to CBs have been identified in the amphibian oocyte nucleus (called sphere organelles) and in insect (called endobodies). CBs are motile and dynamic structures. Both their protein and RNA-protein components can cycle continuously between CBs and other nuclear locations depending on the transcriptional state of the cell.Cajal body http://purl.uniprot.org/locations/31 The PML bodies are dynamic nuclear protein aggregates interspersed between chromatin. These punctate nuclear structures are call PML bodies because the PML gene is essential for their formation. These discrete nuclear foci, 0.2-1.0 micrometer wide, are present in most mammalian cell nuclei and typically number 1 to 30 bodies per nucleus, depending on the cell type, cell-cycle phase and differentiation stage. Recent evidence implies that, although they appear to be uniform, PML-NBs are structurally and functionally heterogeneous and are dynamic structures.PML body http://purl.uniprot.org/locations/465 The nuclear speckles are small subnuclear membraneless organelles or structures, also called the splicing factor (SF) compartments that correspond to nuclear domains located in interchromatin regions of the nucleoplasm of mammalian cells. Protein found in speckles serves as a reservoir of factors that participate in transcription and pre-mRNA processing. Speckles appear, at the immunofluorescence-microscope level, as irregular, punctuate structures, which vary in size and shape. Usually 25-50 speckles are observed per interphase mammalian nucleus. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called interchromatin granules clusters (IGCs). Speckles are dynamic structures. Both their protein and RNA-protein components can cycle continuously between speckles and other nuclear locations depending on the transcriptional state of the cell. Structures similar to nuclear speckles have been identified in the amphibian oocyte nucleus (called B snurposomes) and in Drosophila melanogaster embryos, but not in yeast.Nucleus speckle http://purl.uniprot.org/locations/186 http://purl.uniprot.org/locations/494 The nucleolus is a non-membrane bound nuclear compartment found in eukaryotic cells which is the site of ribosome biogenesis. The interphase nucleolus is organized around the tandemly repeated genes for preribosomal RNA (rRNA). It is composed of at least 2 sub-compartments: the dense fibrillar component (DFC, also called pars fibrosa) and the granular component (GC or pars granulosa). The DFC contains newly synthesized preribosomal RNA and a collection of proteins; the GC is made up of nearly completed preribosomal particles destined for the cytoplasm. In most metazoans, but generally not in lower eukaryotes, a third component, the fibrillar center (FC), can be seen. Plant and animal nuclei can contain more than one nucleolus.Nucleolus http://purl.uniprot.org/locations/188 The nuclear lamina is a meshwork of intermediate filament proteins called lamins and lamin-binding proteins that are embedded in the inner nuclear membrane.Nucleus lamina http://purl.uniprot.org/locations/180 http://purl.uniprot.org/locations/191The inner membrane of the nucleus is the membrane which separates the nuclear matrix from the intermembrane space. In mammals, the inner nuclear membrane is associated with heterochromatin and the nuclear lamina.Nucleus inner membraneThe outer membrane of the nucleus is the membrane facing the cytoplasm. In mammals, the outer nuclear membrane is continuous in many places with the rough endoplasmic reticulum and is dotted with ribosomes.Nucleus outer membrane The mitochondrion is a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. The size and coding capacity of the mitochondrial DNA varies considerably in different organisms, and encodes rRNAs, tRNAs and essential mitochondrial proteins.Mitochondrion http://purl.uniprot.org/locations/173The inner membrane of a mitochondrion is the membrane which separates the mitochondrial matrix from the intermembrane space.Mitochondrion inner membraneThe membrane surrounding a mitochondrion. This term is used when it is not known if the protein is found in or associated with the inner or outer mitochondrial membrane.Mitochondrion membraneThe outer membrane of a mitochondrion is the mitochondrial membrane facing the cytoplasm.Mitochondrion outer membrane The endoplasmic reticulum (ER) is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products. The membrane is a continuation of the outer nuclear membrane, it encloses the cytosol cisternal spaces (or internal lumen), which are continuous with the nuclear periplasmic space. The ER sustains many general functions, including protein synthesis, protein modification, protein folding, insertion of membrane proteins, sequestration of calcium, production of phospholipids and steroids and transport of proteins destined for membranes and secretion.Endoplasmic reticulum The smooth endoplasmic reticulum (SER) is the portion of the ER which is free of ribosomes.Smooth endoplasmic reticulum http://purl.uniprot.org/locations/248The membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membrane The rough endoplasmic reticulum (RER) is the portion of the ER which is covered with ribosomes.Rough endoplasmic reticulum http://purl.uniprot.org/locations/235The membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane http://purl.uniprot.org/locations/95The membrane surrounding the endoplasmic reticulum (ER). The endoplasmic reticulum is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products.Endoplasmic reticulum membraneThe membrane surrounding the microsome.Microsome membraneThe membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membraneThe membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane The Golgi apparatus is a series of flattened, cisternal membranes and similar vesicles usually arranged in close apposition to each other to form stacks. In mammalian cells, the Golgi apparatus is juxtanuclear, often pericentriolar. The stacks are connected laterally by tubules to create a perinuclear ribbon structure, the 'Golgi ribbon'. In plants and lower animal cells, the Golgi exists as many copies of discrete stacks dispersed throughout the cytoplasm. The Golgi is a polarized structure with, in most higher eukaryotic cells, a cis-face associated with a tubular reticular network of membranes facing the endoplasmic reticulum, the cis-Golgi network (CGN), a medial area of disk-shaped flattened cisternae, and a trans-face associated with another tubular reticular membrane network, the trans-Golgi network (TGN) directed toward the plasma membrane and compartments of the endocytic pathway. The Golgi apparatus receives the entire output of de novo synthesized polypeptides from the ER, and functions to posttranslationally process and sort them within vesicles destined to their proper final destination (e.g. plasma membrane, endosomes, lysosomes).Golgi apparatus The trans-Golgi network is a highly dynamic series of interconnected tubules and vesicles at the trans face of the Golgi stack. The trans-Golgi network functions in the processing and sorting of glycoproteins and glycolipids at the interface of the biosynthetic and endosomal pathways. The generation and maintenance of apical and basolateral membranes rely on sorting events that occur in the TGN.trans-Golgi network http://purl.uniprot.org/locations/266The membrane surrounding the trans-Golgi network.trans-Golgi network membrane The Golgi stack consist of a series of flattened curved and parallel series saccules, called cisternae or dictyosomes, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.Golgi stack http://purl.uniprot.org/locations/135The membrane surrounding the Golgi stack.Golgi stack membrane The cis-Golgi network is an extensive tubulovesicular network bound to the cis face of the Golgi stack and which function is to receive process the biosynthetic output from the ER.cis-Golgi network http://purl.uniprot.org/locations/67The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membrane http://purl.uniprot.org/locations/132The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membraneThe membrane surrounding the Golgi apparatus.Golgi apparatus membraneThe membrane surrounding the Golgi stack.Golgi stack membraneThe membrane surrounding the trans-Golgi network.trans-Golgi network membrane The porosome is an actin-regulated dynamic structure at the cell membrane, where membrane-bound secretory vesicles dock and fuse to release their contents.Porosome http://purl.uniprot.org/locations/218 A cell projection is a cell protrusion such as pseudopodium, filopodium, lamellipodium, growth cone, flagellum, acrosome, axon, or bacterial comet tail. These membrane-cytoskeleton-coupled processes are involved in many biological functions, such as cell motility, cancer-cell invasion, endocytosis, phagocytosis, exocytosis, pathogen infection, neurite extension and cytokinesis.Cell projection The filopodium is a thin, tubular, finger-like cell protrusion filled with straight bundled, crosslinked actin filaments having their barbed ends directed towards the cell membrane. Filopodium are observed at the advancing front of the migrating cell and are implicated in cell motility as well as in cell-substrate adhesion. Filopodia explore the environment and form nascent adhesive structures in response to external signaling cues. These long and highly dynamic protrusions, which can extend and retract, are involved in mesenchymal migration. They are observed in many cell types, such as amoebae, keratinocytes, fibroblasts and in neurite growth cones.Filopodium http://purl.uniprot.org/locations/286 The flagellum is a long whip-like or feathery structure which propels the cell through a liquid medium. This motile cilium is produced by the unicellular eukaryotes, and by the motile male gametes of many eukaryotic organisms. The flagella commonly have a characteristic axial '9+2' microtubular array (axoneme) and bends are generated along the length of the flagellum by restricted sliding of the nine outer doublets.Flagellum The basal body is a barrel-shaped microtubule-based structure required for the formation of flagella. Basal bodies, structuraly related to and often interconvertible with centrioles, serves as a nucleation site for axoneme growth.Flagellum basal body http://purl.uniprot.org/locations/308 The flagellum axoneme is the most prominent structural component of the flagellum, which is a long whip-like or feathery structure which propels the cell through a liquid medium. The flagellum axoneme consists of a characteristic axial '9+2' microtubular array.Flagellum axoneme http://purl.uniprot.org/locations/114 http://purl.uniprot.org/locations/117 A ruffle is a cell protrusion at the leading edge of a crawling cell. Ruffles are supported by a microfilament meshwork.Ruffle http://purl.uniprot.org/locations/300 http://purl.uniprot.org/locations/280 The hydrogenosome is a redox organelle of anaerobic unicellular eukaryotes which contains hydrogenase and produces hydrogen and ATP by glycolysis. They are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Most hydrogenosomes lack a genome, but some like that of the anaerobic ciliate Nyctotherus ovalis, have retained a rudimentary genome.Hydrogenosome http://purl.uniprot.org/locations/145The membrane surrounding the hydrogenosome, a redox organelle found in anaerobic unicellular eukaryotes.Hydrogenosome membrane The peroxisome is a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions. Contains mainly peroxidases, several other oxidases and catalase. The catalase regulates the contents of the produced toxic hydrogen peroxide thus protecting the cell. Beta-oxidation of fatty acids is another major function of peroxisomes. In plants and fungi this degradation occurs only in this cellular compartment.Peroxisome The glycosome is a specialized peroxisome found in all members of the protist order Kinetoplastida examined. Nine enzymes involved in glucose and glycerol metabolism are associated with these organelles. These enzymes are involved in pathways which, in other organisms, are usually located in the cytosol.Glycosome http://purl.uniprot.org/locations/129The membrane surrounding the the glycosome, a specialized peroxisome found in all members of the protist order Kinetoplastida examined.Glycosome membrane http://purl.uniprot.org/locations/204The membrane surrounding the the glycosome, a specialized peroxisome found in all members of the protist order Kinetoplastida examined.Glycosome membraneThe membrane surrounding the glyoxysome, a plant peroxisome, especially found in germinating seeds, involved in the breakdown and conversion of fatty acids to acetyl-CoA for the glyoxylate bypass.Glyoxysome membraneThe membrane surrounding a peroxysome.Peroxisome membrane The melanosome is a melanin-containing organelle found in melanocytes and melanophores. Fish and amphibians possess specialized cells, called melanophores, which contain hundreds of melanin-filled pigment granules, termed melanosomes. The sole function of these cells is pigment aggregation in the center of the cell or dispersion throughout the cytoplasm. This alternative transport of pigment allows the animal to effect color changes important for camouflage and social interactions. Melanophores transport their pigment in response to extracellular cues: neurotransmitters in the case of fish and hormonal stimuli in the case of frogs. In both cases, melanosome dispersion is induced by elevation of intracellular cAMP levels, while aggregation is triggered by depression of cAMP. The regulatory mechanisms downstream of these second-messengers are poorly understood. Mammalian melanocytes also produce melanosomes but, unlike melanophores, pigment in these cells is transported to the cell periphery for subsequent exocytosis to surrounding epithelial cells.Melanosome http://purl.uniprot.org/locations/161The membrane surrounding a melanosome.Melanosome membrane A contractile vacuole (CV) complex is a membrane-bound osmoregulatory organelle of fresh water and soil amoebae and protozoa which segregates excess cytosolic water, acquired osmotically, and expel it to the cell exterior, so that the cytosolic osmolarity is kept constant under a given osmotic condition. Depending on the organism, the CV complex (CVC) shows different degrees of specialization of its tubular and vesicular elements. In the most elaborate CVCs of certain ciliates, e.g. Paramecium, a central vacuole, the contractile vacuole or cisterna, is surrounded by radially oriented ampullae or radial arms. These ampullae are connected to a network of channels. Excess cytosolic water, acquired osmotically, is segregated by the radial arms and enters the vacuole, so that the vacuole swells (the fluid-filling phase). The vacuole then rounds (the rounding phase) and the radial arms sever from the vacuole. The vacuole membrane then fuses with the plasma membrane at the pore region and the pore opens. The vacuole shrinks as its fluid is discharged through the pore (the fluid-discharging phase). The pore closes when the fluid has been discharged. The radial arms then reattach to the vacuole, so that the vacuole swells again as the fluid enters from the arms (the next fluid-filling phase).Contractile vacuole http://purl.uniprot.org/locations/73The membrane surrounding a contractile vacuole. A contractile vacuole (CV) complex is a membrane-bound osmoregulatory organelle of fresh water and soil amoebae and protozoa which segregates excess cytosolic water, acquired osmotically, and expel it to the cell exterior, so that the cytosolic osmolarity is kept constant under a given osmotic condition.Contractile vacuole membrane The autophagosome is a double membrane vesicle involved in the degradation of long-lived proteins, unnecessary or damaged organelles as well as other cellular constituents such as lipids or carbohydrates. Crescent-shape isolation membranes or phagophores can sequester cytoplasm and organelles giving rise to autophagosomes. The outer membrane of the autophagosomes then fuse with vacuoles and/or lysosomes and the inner membrane vesicles (termed autophagic bodies) are released into the vacuole/lysosome lumen. These vesicles are then lysed and the contents are degraded by resident hydrolases.Autophagosome http://purl.uniprot.org/locations/23The membrane surrounding the autophagosome.Autophagosome membrane COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle http://purl.uniprot.org/locations/75The membrane surrounding a COPI-coated vesicle. COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle membrane COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle http://purl.uniprot.org/locations/77The membrane surrounding a COPII-coated vesicle. COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle membrane The ER-Golgi intermediate compartment is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites. The ERGIC mediates transport between the endoplasmic reticulum and the Golgi and is the first anterograde/retrograde sorting station in the secretory pathway. ERGIC has not been observed in yeast and plants.Endoplasmic reticulum-Golgi intermediate compartment http://purl.uniprot.org/locations/98The membrane surrounding the ER-Golgi intermediate compartment, which is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites.Endoplasmic reticulum-Golgi intermediate compartment membrane Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface. They also receive newly synthesised proteins destined for vacuolar/lysosomal compartments. In certain cell types, endosomal multivesicular bodies may fuse with the cell surface in an exocytic manner. These released vesicles are called exosomes.Endosome Late endosomes are pleiomorphic with cisternal, tubular and multivesicular regions. They are found in juxtanuclear regions and concentrated at the microtubule organizing center. They are an important sorting station in the endocytic pathway. Recycling to the plasma membrane and to the Golgi occurs in late endosomes. More acidic than early endosomes they are also loaded more slowly in a range of 4 to 30 minutes depending on the cell type. They can be distinguished from lysosome for their enrichment in M6PR.Late endosome http://purl.uniprot.org/locations/152The membrane surrounding the late endosomes.Late endosome membrane Early endosomes form a tubulovesicular network spread throughout the cortical cytoplasm of the cell. Early endosomes are the primary sorting station in the endocytic pathway from which endocytosed molecules can be recycled back to the cell membrane or targeted to degradation in the lysosomes. Loaded by endocytosed molecules in 1 to 4 minutes, their acidic luminal pH around 6.0 allows ligand release from recycling receptors.Early endosome http://purl.uniprot.org/locations/94The membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membrane The multivesicular bodies are a type of late endosome containing internal vesicles formed following the inward budding of the outer endosomal membrane. The contents of the MVBs are then released into the lysosome lumen. The proteins found in the limiting membrane of MVBs are recycled to other compartments.Multivesicular body http://purl.uniprot.org/locations/174The membrane surrounding the multivesicular bodies.Multivesicular body membrane http://purl.uniprot.org/locations/101The membrane surrounding the endosome. Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface.Endosome membraneThe membrane surrounding the late endosomes.Late endosome membraneThe membrane surrounding the recycling endosomes.Recycling endosome membraneThe membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membraneThe membrane surrounding the multivesicular bodies.Multivesicular body membrane The caveola is a small (apparently) uncoated pit mostly found in the cell membrane of many highly differentiated mammalian cells, such as adipocytes, endothelial cells and muscle cells. These flask-shaped invaginations are defined by the presence of caveolins and contains a subset of lipid-raft components, including cholesterol and sphingolipids. Caveolae each comprise a caveolar bulb with a diameter of 60-80 nm, connected to an opening of fairly constant diameter. Caveolae might exists as single pits or can form a cluster of caveolae with non-caveolar membrane between the pits. In many tissues, and particularly in adipocytes, multiple caveolae are arranged around a central vacuolar domain. In developing muscle fibres, multiple caveolae are connected by a single neck to the cell membrane, producing large chains of interconnected caveolae. Another structural feature of caveolae in certain endothelia is the presence of a stomatal diaphragm, which consists of a central density and radial spikes, in the neck of the caveolae. Mature caveolae might be assembled in the Golgi apparatus. Caveolae can flatten out into the cell membrane, thereby loosing their caveolar identity.Caveola http://purl.uniprot.org/locations/35 Clathrin coated vesicles (CCVs) mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle http://purl.uniprot.org/locations/70The membrane surrounding a clathrin-coated vesicle (CCV). CCVs mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle membrane Coated pits are regions of the donor membrane where the assembly of the vesicle coat take place. The coat assembles from soluble protomers such as coat protein complex-I and coat protein complex-II. The components of the coat often define the intracellular sorting station, and contribute to both membrane deformation and local movement of the resulting transport intermediate following scission. During the first steps of the vesicle-mediated membrane transport, coated pits are internalized to form coated vesicles which transport proteins between distinct membrane-bound organelles.Coated pit Coated pits are regions of the cell membrane specialized in receptor-mediated endocytosis. Their cytoplasmic surface is coated with a bristlelike structure made of clathrin. During the first steps of endocytosis, clathrin-coated pits are internalized to form clathrin-coated vesicles which transport proteins from organelle to organelle.Clathrin-coated pit http://purl.uniprot.org/locations/69 http://purl.uniprot.org/locations/72 The lysosome is a membrane-limited organelle present in all eukaryotic cells, which contains a large number of hydrolytic enzymes that are used for degrading almost any kind of cellular constituent, including entire organelles. The mechanisms responsible for delivering cytoplasmic cargo to the lysosome/vacuole are known collectively as autophagy and play an important role in the maintenance of homeostasis.Lysosome A specialized secretory lysosome that is present in cells with cytolytic capability such as cytotoxic T lymphocytes and natural killer cells. Cytolytic granules mediate the storage and regulated excretion of lytic molecules for killing of target cells.Cytolytic granule http://purl.uniprot.org/locations/543The cytolytic granule membrane is the membrane surrounding a cytolytic granule.Cytolytic granule membrane http://purl.uniprot.org/locations/158The cytolytic granule membrane is the membrane surrounding a cytolytic granule.Cytolytic granule membraneThe membrane surrounding a lysosome.Lysosome membrane Cup-shaped invaginations of the cell membrane that subsequently close at their distal margins to form phagosomes during phagocytosis. By progression of its rim along the particle surface, this phagocytic cup envelops and eventually encloses the particle by separation of the phagosome membrane from the cell membrane. Filamentous actin accumulates between the outer and inner leaflet of the cup membrane and is most strongly enriched at the rim of the cup, the site of its protrusion.Phagocytic cup http://purl.uniprot.org/locations/473 The phagosome is a phagocytic cell-specific compartment. These large endocytic membrane-bound vesicles form upon ingestion by the cell of extracellular materials.Phagosome http://purl.uniprot.org/locations/206The membrane surrounding a phagosome.Phagosome membrane The lipid droplet is a dynamic cytoplasmic organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. Lipid droplets may play a role in lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.Lipid droplet http://purl.uniprot.org/locations/154 A chromaffin granule is a specialized secretory vesicle characteristic of chromaffin cells.Chromaffin granule http://purl.uniprot.org/locations/61The chromaffin granule membrane is the membrane surrounding a chromaffin granule, a specialized secretory vesicle characteristic of chromaffin cells.Chromaffin granule membrane Protein found in or associated with cytoplasmic granules.Cytoplasmic granule http://purl.uniprot.org/locations/281The membrane surrounding a cytoplasmic granule.Cytoplasmic granule membrane The trichocyst is an architecturally complex secretory granule having a highly constrained shape docked at specialized cortical sites in Paramecium and other ciliates. Each cell bears about 1'000 trichocysts, which are supposed to be defensive organelles against predators. Trichocyst consists of a spindle-shaped body bearing at its wide end a tip often compared to an inverted golf tee. An external stimulus can trigger massive and synchronous exocytosis. After exocytotic membrane fusion, contact with the H2O and calcium ions in the external medium leads to an extremely rapid (< 50 ms) and irreversible expansion of the trichocyst contents, to yield a second, needle-shaped form which remains insoluble.Trichocyst http://purl.uniprot.org/locations/268 The plastid is a semi-autonomous, self-reproducing organelle. Plastids are remnants of a photosynthetic organism that was engulfed by the host, although not all are now photosynthetic. Plastid genomes encode genes for rRNAs, tRNAs and between about 28 and 150 proteins. Plastids can be categorized in 4 main groups: chloroplasts, cyanelles, apicoplasts and non-photosynthetic. The latter are found is some land plants (Epifagus virginiana), chlorophyte algae (Prototheca wickerhamii) and euglenoids (Astasis longa), which do not encode the genes necessary for photosynthesis and so are not photosynthetic but still contain a plastid. Non-photosynthetic plastids probably do not contain thylakoids.Plastid A cyanelle is a photosynthetic organelle of glaucocystophyte algae. Cyanelles are surrounded by a double membrane and, in between, a peptidoglycan wall. Thylakoid membrane architecture is cyanobacteria-like. Historically, the term cyanelle is derived from a classification as endosymbiotic cyanobacteria, and thus is not fully correct.Cyanelle http://purl.uniprot.org/locations/82The inner membrane of a cyanelle is the membrane which separates the cyanelle stroma from the intermembrane space.Cyanelle inner membraneThe outer membrane of a cyanelle is the cyanelle membrane facing the cytoplasm.Cyanelle outer membraneThe membrane surrounding a cyanelle, a photosynthetic organelle of glaucocystophyte algae. Also used when it is not clear in which cyanelle membrane (outer membrane, inner membrane or thylakoid) a protein is found.Cyanelle membraneThe lipid bilayer membrane of any thylakoid within a cyanelle, a photosynthetic organelle of glaucocystophyte algae.Cyanelle thylakoid membrane The most common form of plastid, the chloroplast is a photosynthetic organelle found in all photosynthetic eukaryotes except glaucocystophyte algae (where it is called a cyanelle) and Paulinella species (where it is called an organellar chromatophore). In green (photosynthetic) tissue they house the machinery necessary for pigment biosynthesis, amino acid synthesis, lipid metabolism etc, as well as the machinery for photosynthesis and CO(2) fixation. They are surrounded by between 2 and 4 membranes and contain thylakoids in green tissue.Chloroplast http://purl.uniprot.org/locations/49The inner membrane of a chloroplast is the membrane which separates the chloroplast stroma from the intermembrane space.Chloroplast inner membraneThe membrane surrounding a chloroplast. Also used when it is not clear in which chloroplast membrane (outer membrane, inner membrane or thylakoid) a protein is found.Chloroplast membraneThe outer membrane of a chloroplast is the chloroplast membrane facing the cytoplasm.Chloroplast outer membraneThe thylakoid membranes of a chloroplast is an internal system of interconnected membranes, that carry out the light reactions of photosynthesis. They are arranged into stacked and unstacked regions called grana and stroma thylakoids, respectively, that are differentially enriched in photosystem I and II complexes. Although extensive, the thylakoid network in an individual chloroplast is thought to comprise a single lumenal compartment.Chloroplast thylakoid membrane The organellar chromatophore is the photosynthetic inclusion found in Paulinella species, which are photosynthetic thecate amoeba. It probably derives from a different endosymbiotic event than that which led to all other plastids. Houses the machinery necessary for photosynthesis and CO(2) fixation and may also be able to make a few amino acids, some fatty acids and a few cofactors. They are surrounded by 2 membranes, between which is found a residual peptidoglycan wall, and contain thylakoids.Organellar chromatophore The internal space enclosed by the organellar chromatophore double membrane but excluding the thylakoid space. This space, filled with a colorless hydrophilic matrix, contains DNA, ribosomes and some temporary products of photosynthesis; other biosynthetic functions that could also occur there include amino acid, fatty acid and some cofactor biosynthesis. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore stromahttp://purl.uniprot.org/locations/353 One of the membranes of an organellar chromatophore. This term is used when it is not known with which membrane (outer membrane, inner membrane or thylakoid) a protein is associated. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore membrane The organellar chromatophore inner membrane is the membrane which separates the chromatophore stroma from the intermembrane space. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore inner membrane http://purl.uniprot.org/locations/359 The organellar chromatophore outer membrane is the organellar chromatophore membrane facing the cytoplasm. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore outer membrane http://purl.uniprot.org/locations/361 http://purl.uniprot.org/locations/352 The thylakoid of an organellar chromatophore is an internal system of interconnected membranes that carry the complexes for the light reactions of photosynthesis. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore thylakoid http://purl.uniprot.org/locations/354The organellar chromatophore thylakoid membrane is an internal system of interconnected membranes that house the complexes which carry out the light reactions of photosynthesis. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore thylakoid membrane http://purl.uniprot.org/locations/351The organellar chromatophore thylakoid membrane is an internal system of interconnected membranes that house the complexes which carry out the light reactions of photosynthesis. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore thylakoid membrane http://purl.uniprot.org/locations/209The inner membrane of a cyanelle is the membrane which separates the cyanelle stroma from the intermembrane space.Cyanelle inner membraneThe membrane surrounding the chromoplast. Also used when it is not clear in which chromoplast membrane (outer membrane, inner membrane or thylakoid) a protein is found.Chromoplast membraneThe outer membrane of a cyanelle is the cyanelle membrane facing the cytoplasm.Cyanelle outer membraneThe organellar chromatophore thylakoid membrane is an internal system of interconnected membranes that house the complexes which carry out the light reactions of photosynthesis. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore thylakoid membraneThe membrane surrounding the etioplast, a plastid found in plants grown in the dark. Also used when it is not clear in which etioplast membrane a protein is found.Etioplast membraneThe inner membrane of an amyloplast.Amyloplast inner membraneThe membrane surrounding the amyloplast. Also used when it is not clear in which amyloplast membrane a protein is found.Amyloplast membraneThe inner membrane of a plastid separates the plastid stroma from the intermembrane space.Plastid inner membraneThe inner membrane of a chloroplast is the membrane which separates the chloroplast stroma from the intermembrane space.Chloroplast inner membraneThe membrane surrounding a cyanelle, a photosynthetic organelle of glaucocystophyte algae. Also used when it is not clear in which cyanelle membrane (outer membrane, inner membrane or thylakoid) a protein is found.Cyanelle membraneThe membrane surrounding a chloroplast. Also used when it is not clear in which chloroplast membrane (outer membrane, inner membrane or thylakoid) a protein is found.Chloroplast membraneThe lipid bilayer membrane of any thylakoid within a cyanelle, a photosynthetic organelle of glaucocystophyte algae.Cyanelle thylakoid membraneThe membrane surrounding or within a plastid. Also used when it is not clear in which plastid membrane (outer membrane, inner membrane or thylakoid) a protein is found.Plastid membraneThe outer membrane of a plastid is the membrane facing the cytoplasm.Plastid outer membraneThe outer membrane of a chloroplast is the chloroplast membrane facing the cytoplasm.Chloroplast outer membraneThe thylakoid membranes of a plastid is an internal system of interconnected membranes found in a plastid.Plastid thylakoid membraneThe thylakoid membranes of a chloroplast is an internal system of interconnected membranes, that carry out the light reactions of photosynthesis. They are arranged into stacked and unstacked regions called grana and stroma thylakoids, respectively, that are differentially enriched in photosystem I and II complexes. Although extensive, the thylakoid network in an individual chloroplast is thought to comprise a single lumenal compartment.Chloroplast thylakoid membrane Spore Protein found in the spore wall. The spore wall is the main element of the spore's resistance to environmental stress. It is usually composed of several layers of different sugar polymers like mannans and glucans which are associated to glycoproteins. The composition, structure and number of layers are very different between bacteria, plants, protozoans or fungi.Spore wall Protein found in the perispore. The perispore corresponds to the outer surface layer of mature bacterial spores and eukaryotic spores. The perispore, also called perine or exosporium, represents the primary contact surface between the spore and environment/host and is a site of spore antigens.Perispore http://purl.uniprot.org/locations/367 Protein found in the spore coat. The spore coat is the thick layer found beneath the perispore of some eukaryotic spores and bacterial mature spores. It is made up of highly cross-linked keratin and layers of specific proteins. The coat is composed of several electron-dense and lamella-like layers, differing between species.Spore coat http://purl.uniprot.org/locations/366 http://purl.uniprot.org/locations/254 Protein found in the spore core. The core also called spore matrix is the central part of the spore and contains normal cell structures, such as DNA, proteins and ribosomes, but is metabolically inactive.Spore core http://purl.uniprot.org/locations/253 Protein associated with the membrane that surrounds the center or core of a spore, often called spore inner membrane in bacterial spores.Spore membrane http://purl.uniprot.org/locations/363 Philippe Le Mercier Eukaryota cell

Trypanosoma Cell: Flagellum

{{< sbp Trypanosoma highlight=flagellum >}}
The cytoplasm is the content of a cell within the plasma membrane and, in eukaryotics cells, surrounding the nucleus. This three-dimensional, jelly-like lattice interconnects and supports the other solid structures. The cytosol (the soluble portion of the cytoplasm outside the organelles) is mostly composed of water and many low molecular weight compounds. In eukaryotes, the cytoplasm also contains a network of cytoplasmic filaments (cytoskeleton).Cytoplasm The cytosol is the unstructured aqueous phase of the cytoplasm excluding organelles, membranes, and insoluble cytoskeletal components.Cytosol http://purl.uniprot.org/locations/91 http://purl.uniprot.org/locations/86 The cell membrane is the selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the cell inner membrane in prokaryotes with 2 membranes.Cell membrane http://purl.uniprot.org/locations/39 The cytoskeleton is a dynamic three-dimensional filamentous structure in the cytoplasm. Its roles include maintenance of cell shape, cell movement (in eukaryotes), cytokinesis, and the organization of organelles or organelle-like structures within the cell. The cytoskeleton includes microfilaments (actin-like proteins), microtubules (tubulin-like proteins), the intermediate filaments (mostly in eukaryotes) and the MinD-ParA proteins, which appear to be unique to prokaryotes.Cytoskeleton The microtubule organizing center (MTOC) is an intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules.Microtubule organizing center The centrosome is a microtubule organizing center (MTOC) responsible for the nucleation and organisation of microtubules. It is composed of two orthogonally arranged centrioles, each one having a barrel shaped microtubule structure, and their surrounding pericentriolar material (PCM).Centrosome Centriolar satellites are nonmembranous, electron-dense and spherical cytoplasmic granules of about 70-100 nm in diameter, occurring around centrosomes in most vertebrate cell types. They contain a number of centrosomal proteins. Centriolar satellites have the ability to move along microtubules, toward their minus ends, i.e. toward centrosomes. Their number increase during interphase and decrease during mitosis.Centriolar satellite http://purl.uniprot.org/locations/485 http://purl.uniprot.org/locations/48 http://purl.uniprot.org/locations/484 http://purl.uniprot.org/locations/90 The nucleus is the most obvious organelle in any eukaryotic cell. It is a membrane-bound organelle surrounded by double membranes which contains most of the cell's genetic material. It communicates with the surrounding cytosol via numerous nuclear pores.Nucleus The nucleoplasm is a highly viscous liquid contained within the nucleus that surrounds the chromosomes and other subnuclear organelles. A network of fibers known as the nuclear matrix can also be found in the nucleoplasm.Nucleoplasm http://purl.uniprot.org/locations/190 The membrane surrounding the nucleus. This term is used when it is not known if the protein is found in or associated with the inner or outer nuclear membrane.Nucleus membrane http://purl.uniprot.org/locations/182 Nuclear body is a collective term for several nuclear, extra-nucleolar, non-membrane-bound sub-compartments, including, but not limited to Cajal bodies, Gemini of Cajal bodies (gems), nuclear speckles and PML bodies. Nuclear bodies are visible as distinct spots in the nucleoplasm. They can vary in number and size depending on the cell line and the type of nuclear body.Nuclear body Gems are nuclear bodies, often found paired or juxtaposed to Cajal bodies, called gems for "gemini of CBs". It is not clear if Cajal bodes and gems are distinct nuclear bodies or if they should be considered as two manifestations of the same structure.Gem http://purl.uniprot.org/locations/127 The nuclear Cajal bodies (CBs) are small subnuclear membraneless organelles present either free in the nucleoplasm and/or physically associated to specific regions of chromatin. CBs contain newly assembled small nuclear ribonucleoproteins (snRNPs) and small nucleolar ribonucleoproteins (snoRNPs) particles, which are involved in pre-mRNA splicing and in ribosomal RNA processing, respectively. Mammalian nucleus in interphase, show 2-6 CBs, as irregular, punctuate structures, which vary in size and shape and which are often juxtaposed to nucleoli. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called coiled body. Structures similar to CBs have been identified in the amphibian oocyte nucleus (called sphere organelles) and in insect (called endobodies). CBs are motile and dynamic structures. Both their protein and RNA-protein components can cycle continuously between CBs and other nuclear locations depending on the transcriptional state of the cell.Cajal body http://purl.uniprot.org/locations/31 The PML bodies are dynamic nuclear protein aggregates interspersed between chromatin. These punctate nuclear structures are call PML bodies because the PML gene is essential for their formation. These discrete nuclear foci, 0.2-1.0 micrometer wide, are present in most mammalian cell nuclei and typically number 1 to 30 bodies per nucleus, depending on the cell type, cell-cycle phase and differentiation stage. Recent evidence implies that, although they appear to be uniform, PML-NBs are structurally and functionally heterogeneous and are dynamic structures.PML body http://purl.uniprot.org/locations/465 The nuclear speckles are small subnuclear membraneless organelles or structures, also called the splicing factor (SF) compartments that correspond to nuclear domains located in interchromatin regions of the nucleoplasm of mammalian cells. Protein found in speckles serves as a reservoir of factors that participate in transcription and pre-mRNA processing. Speckles appear, at the immunofluorescence-microscope level, as irregular, punctuate structures, which vary in size and shape. Usually 25-50 speckles are observed per interphase mammalian nucleus. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called interchromatin granules clusters (IGCs). Speckles are dynamic structures. Both their protein and RNA-protein components can cycle continuously between speckles and other nuclear locations depending on the transcriptional state of the cell. Structures similar to nuclear speckles have been identified in the amphibian oocyte nucleus (called B snurposomes) and in Drosophila melanogaster embryos, but not in yeast.Nucleus speckle http://purl.uniprot.org/locations/186 http://purl.uniprot.org/locations/494 The nucleolus is a non-membrane bound nuclear compartment found in eukaryotic cells which is the site of ribosome biogenesis. The interphase nucleolus is organized around the tandemly repeated genes for preribosomal RNA (rRNA). It is composed of at least 2 sub-compartments: the dense fibrillar component (DFC, also called pars fibrosa) and the granular component (GC or pars granulosa). The DFC contains newly synthesized preribosomal RNA and a collection of proteins; the GC is made up of nearly completed preribosomal particles destined for the cytoplasm. In most metazoans, but generally not in lower eukaryotes, a third component, the fibrillar center (FC), can be seen. Plant and animal nuclei can contain more than one nucleolus.Nucleolus http://purl.uniprot.org/locations/188 The nuclear lamina is a meshwork of intermediate filament proteins called lamins and lamin-binding proteins that are embedded in the inner nuclear membrane.Nucleus lamina http://purl.uniprot.org/locations/180 http://purl.uniprot.org/locations/191The inner membrane of the nucleus is the membrane which separates the nuclear matrix from the intermembrane space. In mammals, the inner nuclear membrane is associated with heterochromatin and the nuclear lamina.Nucleus inner membraneThe outer membrane of the nucleus is the membrane facing the cytoplasm. In mammals, the outer nuclear membrane is continuous in many places with the rough endoplasmic reticulum and is dotted with ribosomes.Nucleus outer membrane The endoplasmic reticulum (ER) is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products. The membrane is a continuation of the outer nuclear membrane, it encloses the cytosol cisternal spaces (or internal lumen), which are continuous with the nuclear periplasmic space. The ER sustains many general functions, including protein synthesis, protein modification, protein folding, insertion of membrane proteins, sequestration of calcium, production of phospholipids and steroids and transport of proteins destined for membranes and secretion.Endoplasmic reticulum The smooth endoplasmic reticulum (SER) is the portion of the ER which is free of ribosomes.Smooth endoplasmic reticulum http://purl.uniprot.org/locations/248The membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membrane The rough endoplasmic reticulum (RER) is the portion of the ER which is covered with ribosomes.Rough endoplasmic reticulum http://purl.uniprot.org/locations/235The membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane http://purl.uniprot.org/locations/95The membrane surrounding the endoplasmic reticulum (ER). The endoplasmic reticulum is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products.Endoplasmic reticulum membraneThe membrane surrounding the microsome.Microsome membraneThe membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membraneThe membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane The mitochondrion is a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. The size and coding capacity of the mitochondrial DNA varies considerably in different organisms, and encodes rRNAs, tRNAs and essential mitochondrial proteins.Mitochondrion The mitochondrial DNA of trypanosomatid protozoa is termed kinetoplast DNA (kDNA). kDNA is a massive network, composed of thousands of topologically interlocked DNA circles. Each cell contains one network condensed into a disk-shaped structure within the matrix of its single mitochondrion. The kDNA circles are of two types, maxicircles present in a few dozen copies and minicircles present in several thousand copies.Kinetoplast http://purl.uniprot.org/locations/150 http://purl.uniprot.org/locations/173The inner membrane of a mitochondrion is the membrane which separates the mitochondrial matrix from the intermembrane space.Mitochondrion inner membraneThe membrane surrounding a mitochondrion. This term is used when it is not known if the protein is found in or associated with the inner or outer mitochondrial membrane.Mitochondrion membraneThe outer membrane of a mitochondrion is the mitochondrial membrane facing the cytoplasm.Mitochondrion outer membrane The Golgi apparatus is a series of flattened, cisternal membranes and similar vesicles usually arranged in close apposition to each other to form stacks. In mammalian cells, the Golgi apparatus is juxtanuclear, often pericentriolar. The stacks are connected laterally by tubules to create a perinuclear ribbon structure, the 'Golgi ribbon'. In plants and lower animal cells, the Golgi exists as many copies of discrete stacks dispersed throughout the cytoplasm. The Golgi is a polarized structure with, in most higher eukaryotic cells, a cis-face associated with a tubular reticular network of membranes facing the endoplasmic reticulum, the cis-Golgi network (CGN), a medial area of disk-shaped flattened cisternae, and a trans-face associated with another tubular reticular membrane network, the trans-Golgi network (TGN) directed toward the plasma membrane and compartments of the endocytic pathway. The Golgi apparatus receives the entire output of de novo synthesized polypeptides from the ER, and functions to posttranslationally process and sort them within vesicles destined to their proper final destination (e.g. plasma membrane, endosomes, lysosomes).Golgi apparatus The trans-Golgi network is a highly dynamic series of interconnected tubules and vesicles at the trans face of the Golgi stack. The trans-Golgi network functions in the processing and sorting of glycoproteins and glycolipids at the interface of the biosynthetic and endosomal pathways. The generation and maintenance of apical and basolateral membranes rely on sorting events that occur in the TGN.trans-Golgi network http://purl.uniprot.org/locations/266The membrane surrounding the trans-Golgi network.trans-Golgi network membrane The Golgi stack consist of a series of flattened curved and parallel series saccules, called cisternae or dictyosomes, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.Golgi stack http://purl.uniprot.org/locations/135The membrane surrounding the Golgi stack.Golgi stack membrane The cis-Golgi network is an extensive tubulovesicular network bound to the cis face of the Golgi stack and which function is to receive process the biosynthetic output from the ER.cis-Golgi network http://purl.uniprot.org/locations/67The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membrane http://purl.uniprot.org/locations/132The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membraneThe membrane surrounding the Golgi apparatus.Golgi apparatus membraneThe membrane surrounding the Golgi stack.Golgi stack membraneThe membrane surrounding the trans-Golgi network.trans-Golgi network membrane The porosome is an actin-regulated dynamic structure at the cell membrane, where membrane-bound secretory vesicles dock and fuse to release their contents.Porosome http://purl.uniprot.org/locations/218 The peroxisome is a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions. Contains mainly peroxidases, several other oxidases and catalase. The catalase regulates the contents of the produced toxic hydrogen peroxide thus protecting the cell. Beta-oxidation of fatty acids is another major function of peroxisomes. In plants and fungi this degradation occurs only in this cellular compartment.Peroxisome The glycosome is a specialized peroxisome found in all members of the protist order Kinetoplastida examined. Nine enzymes involved in glucose and glycerol metabolism are associated with these organelles. These enzymes are involved in pathways which, in other organisms, are usually located in the cytosol.Glycosome http://purl.uniprot.org/locations/129The membrane surrounding the the glycosome, a specialized peroxisome found in all members of the protist order Kinetoplastida examined.Glycosome membrane http://purl.uniprot.org/locations/204The membrane surrounding the the glycosome, a specialized peroxisome found in all members of the protist order Kinetoplastida examined.Glycosome membraneThe membrane surrounding the glyoxysome, a plant peroxisome, especially found in germinating seeds, involved in the breakdown and conversion of fatty acids to acetyl-CoA for the glyoxylate bypass.Glyoxysome membraneThe membrane surrounding a peroxysome.Peroxisome membrane The autophagosome is a double membrane vesicle involved in the degradation of long-lived proteins, unnecessary or damaged organelles as well as other cellular constituents such as lipids or carbohydrates. Crescent-shape isolation membranes or phagophores can sequester cytoplasm and organelles giving rise to autophagosomes. The outer membrane of the autophagosomes then fuse with vacuoles and/or lysosomes and the inner membrane vesicles (termed autophagic bodies) are released into the vacuole/lysosome lumen. These vesicles are then lysed and the contents are degraded by resident hydrolases.Autophagosome http://purl.uniprot.org/locations/23The membrane surrounding the autophagosome.Autophagosome membrane COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle http://purl.uniprot.org/locations/75The membrane surrounding a COPI-coated vesicle. COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle membrane COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle http://purl.uniprot.org/locations/77The membrane surrounding a COPII-coated vesicle. COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle membrane The ER-Golgi intermediate compartment is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites. The ERGIC mediates transport between the endoplasmic reticulum and the Golgi and is the first anterograde/retrograde sorting station in the secretory pathway. ERGIC has not been observed in yeast and plants.Endoplasmic reticulum-Golgi intermediate compartment http://purl.uniprot.org/locations/98The membrane surrounding the ER-Golgi intermediate compartment, which is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites.Endoplasmic reticulum-Golgi intermediate compartment membrane Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface. They also receive newly synthesised proteins destined for vacuolar/lysosomal compartments. In certain cell types, endosomal multivesicular bodies may fuse with the cell surface in an exocytic manner. These released vesicles are called exosomes.Endosome Late endosomes are pleiomorphic with cisternal, tubular and multivesicular regions. They are found in juxtanuclear regions and concentrated at the microtubule organizing center. They are an important sorting station in the endocytic pathway. Recycling to the plasma membrane and to the Golgi occurs in late endosomes. More acidic than early endosomes they are also loaded more slowly in a range of 4 to 30 minutes depending on the cell type. They can be distinguished from lysosome for their enrichment in M6PR.Late endosome http://purl.uniprot.org/locations/152The membrane surrounding the late endosomes.Late endosome membrane Early endosomes form a tubulovesicular network spread throughout the cortical cytoplasm of the cell. Early endosomes are the primary sorting station in the endocytic pathway from which endocytosed molecules can be recycled back to the cell membrane or targeted to degradation in the lysosomes. Loaded by endocytosed molecules in 1 to 4 minutes, their acidic luminal pH around 6.0 allows ligand release from recycling receptors.Early endosome http://purl.uniprot.org/locations/94The membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membrane The multivesicular bodies are a type of late endosome containing internal vesicles formed following the inward budding of the outer endosomal membrane. The contents of the MVBs are then released into the lysosome lumen. The proteins found in the limiting membrane of MVBs are recycled to other compartments.Multivesicular body http://purl.uniprot.org/locations/174The membrane surrounding the multivesicular bodies.Multivesicular body membrane http://purl.uniprot.org/locations/101The membrane surrounding the endosome. Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface.Endosome membraneThe membrane surrounding the late endosomes.Late endosome membraneThe membrane surrounding the recycling endosomes.Recycling endosome membraneThe membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membraneThe membrane surrounding the multivesicular bodies.Multivesicular body membrane The caveola is a small (apparently) uncoated pit mostly found in the cell membrane of many highly differentiated mammalian cells, such as adipocytes, endothelial cells and muscle cells. These flask-shaped invaginations are defined by the presence of caveolins and contains a subset of lipid-raft components, including cholesterol and sphingolipids. Caveolae each comprise a caveolar bulb with a diameter of 60-80 nm, connected to an opening of fairly constant diameter. Caveolae might exists as single pits or can form a cluster of caveolae with non-caveolar membrane between the pits. In many tissues, and particularly in adipocytes, multiple caveolae are arranged around a central vacuolar domain. In developing muscle fibres, multiple caveolae are connected by a single neck to the cell membrane, producing large chains of interconnected caveolae. Another structural feature of caveolae in certain endothelia is the presence of a stomatal diaphragm, which consists of a central density and radial spikes, in the neck of the caveolae. Mature caveolae might be assembled in the Golgi apparatus. Caveolae can flatten out into the cell membrane, thereby loosing their caveolar identity.Caveola http://purl.uniprot.org/locations/35 Clathrin coated vesicles (CCVs) mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle http://purl.uniprot.org/locations/70The membrane surrounding a clathrin-coated vesicle (CCV). CCVs mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle membrane Coated pits are regions of the donor membrane where the assembly of the vesicle coat take place. The coat assembles from soluble protomers such as coat protein complex-I and coat protein complex-II. The components of the coat often define the intracellular sorting station, and contribute to both membrane deformation and local movement of the resulting transport intermediate following scission. During the first steps of the vesicle-mediated membrane transport, coated pits are internalized to form coated vesicles which transport proteins between distinct membrane-bound organelles.Coated pit Coated pits are regions of the cell membrane specialized in receptor-mediated endocytosis. Their cytoplasmic surface is coated with a bristlelike structure made of clathrin. During the first steps of endocytosis, clathrin-coated pits are internalized to form clathrin-coated vesicles which transport proteins from organelle to organelle.Clathrin-coated pit http://purl.uniprot.org/locations/69 http://purl.uniprot.org/locations/72 The lysosome is a membrane-limited organelle present in all eukaryotic cells, which contains a large number of hydrolytic enzymes that are used for degrading almost any kind of cellular constituent, including entire organelles. The mechanisms responsible for delivering cytoplasmic cargo to the lysosome/vacuole are known collectively as autophagy and play an important role in the maintenance of homeostasis.Lysosome http://purl.uniprot.org/locations/158The cytolytic granule membrane is the membrane surrounding a cytolytic granule.Cytolytic granule membraneThe membrane surrounding a lysosome.Lysosome membrane The phagosome is a phagocytic cell-specific compartment. These large endocytic membrane-bound vesicles form upon ingestion by the cell of extracellular materials.Phagosome http://purl.uniprot.org/locations/206The membrane surrounding a phagosome.Phagosome membrane The lipid droplet is a dynamic cytoplasmic organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. Lipid droplets may play a role in lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.Lipid droplet http://purl.uniprot.org/locations/154 Protein found in or associated with cytoplasmic granules.Cytoplasmic granule http://purl.uniprot.org/locations/281The membrane surrounding a cytoplasmic granule.Cytoplasmic granule membrane A cell projection is a cell protrusion such as pseudopodium, filopodium, lamellipodium, growth cone, flagellum, acrosome, axon, or bacterial comet tail. These membrane-cytoskeleton-coupled processes are involved in many biological functions, such as cell motility, cancer-cell invasion, endocytosis, phagocytosis, exocytosis, pathogen infection, neurite extension and cytokinesis.Cell projection The flagellum is a long whip-like or feathery structure which propels the cell through a liquid medium. This motile cilium is produced by the unicellular eukaryotes, and by the motile male gametes of many eukaryotic organisms. The flagella commonly have a characteristic axial '9+2' microtubular array (axoneme) and bends are generated along the length of the flagellum by restricted sliding of the nine outer doublets.Flagellum The basal body is a barrel-shaped microtubule-based structure required for the formation of flagella. Basal bodies, structuraly related to and often interconvertible with centrioles, serves as a nucleation site for axoneme growth.Flagellum basal body http://purl.uniprot.org/locations/308 The flagellum axoneme is the most prominent structural component of the flagellum, which is a long whip-like or feathery structure which propels the cell through a liquid medium. The flagellum axoneme consists of a characteristic axial '9+2' microtubular array.Flagellum axoneme http://purl.uniprot.org/locations/114 http://purl.uniprot.org/locations/117 http://purl.uniprot.org/locations/280 Philippe Le Mercier Trypanosoma cell

Fungal Cell: Nucleus

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Protein located outside the cell membrane(s).Secreted The extracellular space is the space outside of the cell membrane but part of a multicellular organism. The term is typically used for a secreted protein that remains associated with the cell, e.g. as part of the extracellular matrix. It is not used for a protein that is secreted into the blood stream (or other body fluids) of eukaryotic, multicellular organisms, such as insulin or fibroblast growth factors.Extracellular space http://purl.uniprot.org/locations/112 http://purl.uniprot.org/locations/243 The cytoplasm is the content of a cell within the plasma membrane and, in eukaryotics cells, surrounding the nucleus. This three-dimensional, jelly-like lattice interconnects and supports the other solid structures. The cytosol (the soluble portion of the cytoplasm outside the organelles) is mostly composed of water and many low molecular weight compounds. In eukaryotes, the cytoplasm also contains a network of cytoplasmic filaments (cytoskeleton).Cytoplasm The cytosol is the unstructured aqueous phase of the cytoplasm excluding organelles, membranes, and insoluble cytoskeletal components.Cytosol http://purl.uniprot.org/locations/91 http://purl.uniprot.org/locations/86 The complex and rigid layer surrounding the cell. Cell walls are found in bacteria, archaea, fungi, plants, and algae. The cell wall envelopes the inner or plasma membrane in all bacteria and is surrounded by the outer membrane in bacteria with 2 membranes (Gram-negative). Bacterial cell walls contain peptidoglycan while those of archaea are not made of peptidoglycan, but some archaea may contain pseudopeptidoglycan, which is composed of N-acetyltalosaminuronic acid, instead of N-acetyl muramic acid in peptidoglycan. The plant cell wall is made of fibrils of cellulose embedded in a matrix of several other kinds of polymers such as pectin and lignin. Algal cell walls are usually composed of cellulose, glycoproteins, sporopollenin, calcium and various polysaccharides such as manosyl, xylanes, alginic acid. Diatom cell walls (or frustules) contain silica. The cell wall plays a role in cell shape, cell stability and development, and protection against environmental dangers.Cell wall http://purl.uniprot.org/locations/41 The perinuclear region is the cytoplasmic region just around the nucleus.Perinuclear region http://purl.uniprot.org/locations/198 The region at either end of the longest axis of a cylindrical or elongated cell, where polarized growth may occur.Cell tip http://purl.uniprot.org/locations/456 The cell membrane is the selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the cell inner membrane in prokaryotes with 2 membranes.Cell membrane http://purl.uniprot.org/locations/39 The mitochondrion is a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. The size and coding capacity of the mitochondrial DNA varies considerably in different organisms, and encodes rRNAs, tRNAs and essential mitochondrial proteins.Mitochondrion http://purl.uniprot.org/locations/173The inner membrane of a mitochondrion is the membrane which separates the mitochondrial matrix from the intermembrane space.Mitochondrion inner membraneThe membrane surrounding a mitochondrion. This term is used when it is not known if the protein is found in or associated with the inner or outer mitochondrial membrane.Mitochondrion membraneThe outer membrane of a mitochondrion is the mitochondrial membrane facing the cytoplasm.Mitochondrion outer membrane The cytoskeleton is a dynamic three-dimensional filamentous structure in the cytoplasm. Its roles include maintenance of cell shape, cell movement (in eukaryotes), cytokinesis, and the organization of organelles or organelle-like structures within the cell. The cytoskeleton includes microfilaments (actin-like proteins), microtubules (tubulin-like proteins), the intermediate filaments (mostly in eukaryotes) and the MinD-ParA proteins, which appear to be unique to prokaryotes.Cytoskeleton The actin patch is a highly dynamic actin structure in fungi required primarily for endocytosis but possibly also coupled to exocytosis. Actin patches are highly motile, they first assemble at sites of polarized cell growth and then move slowly and nondirectionally along the cell cortex.Actin patch http://purl.uniprot.org/locations/8 http://purl.uniprot.org/locations/90 The endoplasmic reticulum (ER) is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products. The membrane is a continuation of the outer nuclear membrane, it encloses the cytosol cisternal spaces (or internal lumen), which are continuous with the nuclear periplasmic space. The ER sustains many general functions, including protein synthesis, protein modification, protein folding, insertion of membrane proteins, sequestration of calcium, production of phospholipids and steroids and transport of proteins destined for membranes and secretion.Endoplasmic reticulum http://purl.uniprot.org/locations/95The membrane surrounding the endoplasmic reticulum (ER). The endoplasmic reticulum is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products.Endoplasmic reticulum membraneThe membrane surrounding the microsome.Microsome membraneThe membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membraneThe membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane The nucleus is the most obvious organelle in any eukaryotic cell. It is a membrane-bound organelle surrounded by double membranes which contains most of the cell's genetic material. It communicates with the surrounding cytosol via numerous nuclear pores.Nucleus The nucleoplasm is a highly viscous liquid contained within the nucleus that surrounds the chromosomes and other subnuclear organelles. A network of fibers known as the nuclear matrix can also be found in the nucleoplasm.Nucleoplasm http://purl.uniprot.org/locations/190 The nuclear lamina is a meshwork of intermediate filament proteins called lamins and lamin-binding proteins that are embedded in the inner nuclear membrane.Nucleus lamina http://purl.uniprot.org/locations/180 The nucleolus is a non-membrane bound nuclear compartment found in eukaryotic cells which is the site of ribosome biogenesis. The interphase nucleolus is organized around the tandemly repeated genes for preribosomal RNA (rRNA). It is composed of at least 2 sub-compartments: the dense fibrillar component (DFC, also called pars fibrosa) and the granular component (GC or pars granulosa). The DFC contains newly synthesized preribosomal RNA and a collection of proteins; the GC is made up of nearly completed preribosomal particles destined for the cytoplasm. In most metazoans, but generally not in lower eukaryotes, a third component, the fibrillar center (FC), can be seen. Plant and animal nuclei can contain more than one nucleolus.Nucleolus http://purl.uniprot.org/locations/188 Nuclear body is a collective term for several nuclear, extra-nucleolar, non-membrane-bound sub-compartments, including, but not limited to Cajal bodies, Gemini of Cajal bodies (gems), nuclear speckles and PML bodies. Nuclear bodies are visible as distinct spots in the nucleoplasm. They can vary in number and size depending on the cell line and the type of nuclear body.Nuclear body The PML bodies are dynamic nuclear protein aggregates interspersed between chromatin. These punctate nuclear structures are call PML bodies because the PML gene is essential for their formation. These discrete nuclear foci, 0.2-1.0 micrometer wide, are present in most mammalian cell nuclei and typically number 1 to 30 bodies per nucleus, depending on the cell type, cell-cycle phase and differentiation stage. Recent evidence implies that, although they appear to be uniform, PML-NBs are structurally and functionally heterogeneous and are dynamic structures.PML body http://purl.uniprot.org/locations/465 The nuclear Cajal bodies (CBs) are small subnuclear membraneless organelles present either free in the nucleoplasm and/or physically associated to specific regions of chromatin. CBs contain newly assembled small nuclear ribonucleoproteins (snRNPs) and small nucleolar ribonucleoproteins (snoRNPs) particles, which are involved in pre-mRNA splicing and in ribosomal RNA processing, respectively. Mammalian nucleus in interphase, show 2-6 CBs, as irregular, punctuate structures, which vary in size and shape and which are often juxtaposed to nucleoli. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called coiled body. Structures similar to CBs have been identified in the amphibian oocyte nucleus (called sphere organelles) and in insect (called endobodies). CBs are motile and dynamic structures. Both their protein and RNA-protein components can cycle continuously between CBs and other nuclear locations depending on the transcriptional state of the cell.Cajal body http://purl.uniprot.org/locations/31 Gems are nuclear bodies, often found paired or juxtaposed to Cajal bodies, called gems for "gemini of CBs". It is not clear if Cajal bodes and gems are distinct nuclear bodies or if they should be considered as two manifestations of the same structure.Gem http://purl.uniprot.org/locations/127 The nuclear speckles are small subnuclear membraneless organelles or structures, also called the splicing factor (SF) compartments that correspond to nuclear domains located in interchromatin regions of the nucleoplasm of mammalian cells. Protein found in speckles serves as a reservoir of factors that participate in transcription and pre-mRNA processing. Speckles appear, at the immunofluorescence-microscope level, as irregular, punctuate structures, which vary in size and shape. Usually 25-50 speckles are observed per interphase mammalian nucleus. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called interchromatin granules clusters (IGCs). Speckles are dynamic structures. Both their protein and RNA-protein components can cycle continuously between speckles and other nuclear locations depending on the transcriptional state of the cell. Structures similar to nuclear speckles have been identified in the amphibian oocyte nucleus (called B snurposomes) and in Drosophila melanogaster embryos, but not in yeast.Nucleus speckle http://purl.uniprot.org/locations/186 http://purl.uniprot.org/locations/494 The membrane surrounding the nucleus. This term is used when it is not known if the protein is found in or associated with the inner or outer nuclear membrane.Nucleus membrane http://purl.uniprot.org/locations/182 The spindle pole body is the microtubule organizing center (MTOC) in fungi, functionally equivalent to the animal cell centrosome. The SPB is responsible for the nucleation and organisation of microtubules. This may include the spindle microtubules required for chromosome segregation in mitosis and meiosis as well as the cytoplasmic interphase microtubules.Spindle pole body http://purl.uniprot.org/locations/252 http://purl.uniprot.org/locations/191The inner membrane of the nucleus is the membrane which separates the nuclear matrix from the intermembrane space. In mammals, the inner nuclear membrane is associated with heterochromatin and the nuclear lamina.Nucleus inner membraneThe outer membrane of the nucleus is the membrane facing the cytoplasm. In mammals, the outer nuclear membrane is continuous in many places with the rough endoplasmic reticulum and is dotted with ribosomes.Nucleus outer membrane The Golgi apparatus is a series of flattened, cisternal membranes and similar vesicles usually arranged in close apposition to each other to form stacks. In mammalian cells, the Golgi apparatus is juxtanuclear, often pericentriolar. The stacks are connected laterally by tubules to create a perinuclear ribbon structure, the 'Golgi ribbon'. In plants and lower animal cells, the Golgi exists as many copies of discrete stacks dispersed throughout the cytoplasm. The Golgi is a polarized structure with, in most higher eukaryotic cells, a cis-face associated with a tubular reticular network of membranes facing the endoplasmic reticulum, the cis-Golgi network (CGN), a medial area of disk-shaped flattened cisternae, and a trans-face associated with another tubular reticular membrane network, the trans-Golgi network (TGN) directed toward the plasma membrane and compartments of the endocytic pathway. The Golgi apparatus receives the entire output of de novo synthesized polypeptides from the ER, and functions to posttranslationally process and sort them within vesicles destined to their proper final destination (e.g. plasma membrane, endosomes, lysosomes).Golgi apparatus The cis-Golgi network is an extensive tubulovesicular network bound to the cis face of the Golgi stack and which function is to receive process the biosynthetic output from the ER.cis-Golgi network http://purl.uniprot.org/locations/67The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membrane The Golgi stack consist of a series of flattened curved and parallel series saccules, called cisternae or dictyosomes, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.Golgi stack http://purl.uniprot.org/locations/135The membrane surrounding the Golgi stack.Golgi stack membrane The trans-Golgi network is a highly dynamic series of interconnected tubules and vesicles at the trans face of the Golgi stack. The trans-Golgi network functions in the processing and sorting of glycoproteins and glycolipids at the interface of the biosynthetic and endosomal pathways. The generation and maintenance of apical and basolateral membranes rely on sorting events that occur in the TGN.trans-Golgi network http://purl.uniprot.org/locations/266The membrane surrounding the trans-Golgi network.trans-Golgi network membrane http://purl.uniprot.org/locations/132The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membraneThe membrane surrounding the Golgi apparatus.Golgi apparatus membraneThe membrane surrounding the Golgi stack.Golgi stack membraneThe membrane surrounding the trans-Golgi network.trans-Golgi network membrane COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle http://purl.uniprot.org/locations/75The membrane surrounding a COPI-coated vesicle. COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle membrane COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle http://purl.uniprot.org/locations/77The membrane surrounding a COPII-coated vesicle. COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle membrane The ER-Golgi intermediate compartment is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites. The ERGIC mediates transport between the endoplasmic reticulum and the Golgi and is the first anterograde/retrograde sorting station in the secretory pathway. ERGIC has not been observed in yeast and plants.Endoplasmic reticulum-Golgi intermediate compartment http://purl.uniprot.org/locations/98The membrane surrounding the ER-Golgi intermediate compartment, which is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites.Endoplasmic reticulum-Golgi intermediate compartment membrane The vacuole is a generally large fluid-filled membrane-bound compartment in the cytoplasm. The precise form and function of vacuoles may vary between phyla. Plant vacuoles are among the best characterized. They differ in terms of their lumenal contents and processing enzymes, as well as on the basis of the type of integral proteins in their membranes (tonoplast intrinsic proteins, TIPs). Examples include the lytic vacuole, the storage vacuole and the lutoid. One important function of plant vacuoles is the maintenance of hydrostatic pressure. Other eukaryotes employ vacuoles for a variety of purposes, including storage (as in the yeast lysosome/vacuole), secretion and phagocytosis. In Protozoa, contractile vacuoles can be used to discharge water from the cytoplasm to the external environment. Aquatic microorganisms may employ gas vacuoles (composed of clusters of inert gas vesicles) to provide buoyancy.Vacuole http://purl.uniprot.org/locations/272The membrane surrounding a protein storage vacuole.Protein storage vacuole membraneThe membrane surrounding a contractile vacuole. A contractile vacuole (CV) complex is a membrane-bound osmoregulatory organelle of fresh water and soil amoebae and protozoa which segregates excess cytosolic water, acquired osmotically, and expel it to the cell exterior, so that the cytosolic osmolarity is kept constant under a given osmotic condition.Contractile vacuole membraneThe membrane of an aleurone grain.Aleurone grain membraneThe membrane surrounding a gas vesicle.Gas vesicle membraneThe membrane surrounding a vacuole.Vacuole membrane The peroxisome is a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions. Contains mainly peroxidases, several other oxidases and catalase. The catalase regulates the contents of the produced toxic hydrogen peroxide thus protecting the cell. Beta-oxidation of fatty acids is another major function of peroxisomes. In plants and fungi this degradation occurs only in this cellular compartment.Peroxisome http://purl.uniprot.org/locations/204The membrane surrounding the the glycosome, a specialized peroxisome found in all members of the protist order Kinetoplastida examined.Glycosome membraneThe membrane surrounding the glyoxysome, a plant peroxisome, especially found in germinating seeds, involved in the breakdown and conversion of fatty acids to acetyl-CoA for the glyoxylate bypass.Glyoxysome membraneThe membrane surrounding a peroxysome.Peroxisome membrane The autophagosome is a double membrane vesicle involved in the degradation of long-lived proteins, unnecessary or damaged organelles as well as other cellular constituents such as lipids or carbohydrates. Crescent-shape isolation membranes or phagophores can sequester cytoplasm and organelles giving rise to autophagosomes. The outer membrane of the autophagosomes then fuse with vacuoles and/or lysosomes and the inner membrane vesicles (termed autophagic bodies) are released into the vacuole/lysosome lumen. These vesicles are then lysed and the contents are degraded by resident hydrolases.Autophagosome The autophagosome is a double membrane vesicle involved in the degradation of long-lived proteins, unnecessary or damaged organelles as well as other cellular constituents such as lipids or carbohydrates. Crescent-shape isolation membranes or phagophores can sequester cytoplasm and organelles giving rise to autophagosomes. The outer membrane of the autophagosomes then fuse with vacuoles and/or lysosomes and the inner membrane vesicles (termed autophagic bodies) are released into the vacuole/lysosome lumen. These vesicles are then lysed and the contents are degraded by resident hydrolases.Autophagosome http://purl.uniprot.org/locations/23The membrane surrounding the autophagosome.Autophagosome membrane http://purl.uniprot.org/locations/23The membrane surrounding the autophagosome.Autophagosome membrane Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface. They also receive newly synthesised proteins destined for vacuolar/lysosomal compartments. In certain cell types, endosomal multivesicular bodies may fuse with the cell surface in an exocytic manner. These released vesicles are called exosomes.Endosome Late endosomes are pleiomorphic with cisternal, tubular and multivesicular regions. They are found in juxtanuclear regions and concentrated at the microtubule organizing center. They are an important sorting station in the endocytic pathway. Recycling to the plasma membrane and to the Golgi occurs in late endosomes. More acidic than early endosomes they are also loaded more slowly in a range of 4 to 30 minutes depending on the cell type. They can be distinguished from lysosome for their enrichment in M6PR.Late endosome http://purl.uniprot.org/locations/152The membrane surrounding the late endosomes.Late endosome membrane Early endosomes form a tubulovesicular network spread throughout the cortical cytoplasm of the cell. Early endosomes are the primary sorting station in the endocytic pathway from which endocytosed molecules can be recycled back to the cell membrane or targeted to degradation in the lysosomes. Loaded by endocytosed molecules in 1 to 4 minutes, their acidic luminal pH around 6.0 allows ligand release from recycling receptors.Early endosome http://purl.uniprot.org/locations/94The membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membrane http://purl.uniprot.org/locations/101The membrane surrounding the endosome. Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface.Endosome membraneThe membrane surrounding the late endosomes.Late endosome membraneThe membrane surrounding the recycling endosomes.Recycling endosome membraneThe membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membraneThe membrane surrounding the multivesicular bodies.Multivesicular body membrane Late endosomes are pleiomorphic with cisternal, tubular and multivesicular regions. They are found in juxtanuclear regions and concentrated at the microtubule organizing center. They are an important sorting station in the endocytic pathway. Recycling to the plasma membrane and to the Golgi occurs in late endosomes. More acidic than early endosomes they are also loaded more slowly in a range of 4 to 30 minutes depending on the cell type. They can be distinguished from lysosome for their enrichment in M6PR.Late endosome http://purl.uniprot.org/locations/152The membrane surrounding the late endosomes.Late endosome membrane A structure composed of peptidoglycan and often chitin in addition to other materials. It usually forms perpendicular to the long axis of a cell or hypha and grows centripetally from the cell wall to the center of the cell and often functions in the compartmentalization of a cell into two daughter cells.Cell septum http://purl.uniprot.org/locations/455 The lipid droplet is a dynamic cytoplasmic organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. Lipid droplets may play a role in lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.Lipid droplet http://purl.uniprot.org/locations/154 Protein found in or associated with cytoplasmic granules.Cytoplasmic granule http://purl.uniprot.org/locations/281The membrane surrounding a cytoplasmic granule.Cytoplasmic granule membrane Spores are hardy unicellular units used by various bacteria, fungi, plants and protozoa to allow them to remain dormant during long periods of time and under often unfavorable conditions.Spore Spore Protein found in the spore core. The core also called spore matrix is the central part of the spore and contains normal cell structures, such as DNA, proteins and ribosomes, but is metabolically inactive.Spore core Protein associated with the membrane that surrounds the center or core of a spore, often called spore inner membrane in bacterial spores.Spore membrane http://purl.uniprot.org/locations/363 http://purl.uniprot.org/locations/253 Protein found in the spore wall. The spore wall is the main element of the spore's resistance to environmental stress. It is usually composed of several layers of different sugar polymers like mannans and glucans which are associated to glycoproteins. The composition, structure and number of layers are very different between bacteria, plants, protozoans or fungi.Spore wall http://purl.uniprot.org/locations/254 Protein found in the spore coat. The spore coat is the thick layer found beneath the perispore of some eukaryotic spores and bacterial mature spores. It is made up of highly cross-linked keratin and layers of specific proteins. The coat is composed of several electron-dense and lamella-like layers, differing between species.Spore coat http://purl.uniprot.org/locations/366 Protein found in the perispore. The perispore corresponds to the outer surface layer of mature bacterial spores and eukaryotic spores. The perispore, also called perine or exosporium, represents the primary contact surface between the spore and environment/host and is a site of spore antigens.Perispore http://purl.uniprot.org/locations/367 The polar tube is a highly specialised structure unique to Microsporidia and required for host cell invasion. In the spore, the polar tube is connected at the anterior end, and then coils around the sporoplasm. Upon appropriate environmental stimulation, the polar tube rapidly discharges out of the spore, pierces a cell membrane and serves as a conduit for sporoplasm passage into the new host cell.Spore polar tube http://purl.uniprot.org/locations/436 http://purl.uniprot.org/locations/539Protein associated with the spore outer membrane. The outer membrane, also called the cortex membrane, is a membrane localized between the cortex and the inner layer of the coat of bacterial mature spores.Spore outer membrane The prospore or immature spore is formed during sporulation by the engulfment of the post-meiotic nuclei by the prospore double membrane. These prospores are then maturated into spores with the synthesis of the spore wall.Prospore The prospore membrane is a double membrane which forms at the spindle pole body outer plaque during the second meiotic division of the sporulation process. The prospore membrane grows larger and finally engulfs the post-meiotic nuclei to form immature spores called prospores. The de novo synthesis of the spore wall occurs in the prospore intermembrane space and leads to mature spores.Prospore membrane http://purl.uniprot.org/locations/368 http://purl.uniprot.org/locations/369 Philippe Le Mercier Fungal cell

Coccus Cell: Wall

{{< sbp Bacteria2M_coccus highlight=wall >}}
Protein located outside the cell membrane(s).Secreted The extracellular space is the space outside of the cell membrane but part of a multicellular organism. The term is typically used for a secreted protein that remains associated with the cell, e.g. as part of the extracellular matrix. It is not used for a protein that is secreted into the blood stream (or other body fluids) of eukaryotic, multicellular organisms, such as insulin or fibroblast growth factors.Extracellular space http://purl.uniprot.org/locations/112 Extracellular vesicles are vesicles that have been released by cells.Extracellular vesicle http://purl.uniprot.org/locations/499The membrane surrounding an extracellular vesicle.Extracellular vesicle membrane http://purl.uniprot.org/locations/243 The cytoplasm is the content of a cell within the plasma membrane and, in eukaryotics cells, surrounding the nucleus. This three-dimensional, jelly-like lattice interconnects and supports the other solid structures. The cytosol (the soluble portion of the cytoplasm outside the organelles) is mostly composed of water and many low molecular weight compounds. In eukaryotes, the cytoplasm also contains a network of cytoplasmic filaments (cytoskeleton).Cytoplasm The cytosol is the unstructured aqueous phase of the cytoplasm excluding organelles, membranes, and insoluble cytoskeletal components.Cytosol http://purl.uniprot.org/locations/91 http://purl.uniprot.org/locations/86 The cell envelope comprises the cell membrane, the cell wall and an outer membrane if present. In bacteria with 1 membrane (Gram-positive) the cell envelope consists of the cytoplasmic membrane, cell wall and capsule. In bacteria with 2 membranes (Gram-negative) the envelope consists of the cytoplasmic membrane, cell wall, periplasmic space, outer membrane and capsule. The archaeal cell envelope generally consists of single membrane covered by a surface layer (S-layer). Ignicoccus species exceptionally have an outer membrane which encloses a large periplasmic space. Extreme thermophiles and acidophiles have tetraether type glycerophospholipids with C40 isoprenoid chains. The yeast cell envelope is a protecting capsule which consists of the cytoplasmic membrane, the periplasmic space, and the cell wall.Cell envelope The capsule is a protective structure surrounding some bacteria or fungi. The bacterial capsule is a layer of material, usually polysaccharide, attached to the cell wall possibly via covalent attachments to either phospholipid or lipid-A molecules. It has several functions: promote bacterial adhesion to surfaces or interaction with other organisms; act as a permeability barrier, as a defense mechanism against phagocytosis and/or as a nutrient reserve. Among pathogens, capsule formation often correlates with pathogenicity. The fungal capsule is an extracellular layer which lies outside the cell wall and it is usually composed of polysaccharides. It protects the cell from different environmental dangers such as phagocytosis, dessication, etc.Capsule http://purl.uniprot.org/locations/33 The periplasm is the space between the inner and outer membrane in Gram-negative bacteria. In Gram-positive bacteria a smaller periplasmic space is found between the inner membrane and the peptidoglycan layer. Also used for the intermembrane spaces of fungi and organelles.Periplasm http://purl.uniprot.org/locations/200 The prokaryotic inner cell membrane is the selectively permeable membrane which separates the cytoplasm from the periplasm in prokaryotes with 2 membranes.Cell inner membrane http://purl.uniprot.org/locations/37 The complex and rigid layer surrounding the cell. Cell walls are found in bacteria, archaea, fungi, plants, and algae. The cell wall envelopes the inner or plasma membrane in all bacteria and is surrounded by the outer membrane in bacteria with 2 membranes (Gram-negative). Bacterial cell walls contain peptidoglycan while those of archaea are not made of peptidoglycan, but some archaea may contain pseudopeptidoglycan, which is composed of N-acetyltalosaminuronic acid, instead of N-acetyl muramic acid in peptidoglycan. The plant cell wall is made of fibrils of cellulose embedded in a matrix of several other kinds of polymers such as pectin and lignin. Algal cell walls are usually composed of cellulose, glycoproteins, sporopollenin, calcium and various polysaccharides such as manosyl, xylanes, alginic acid. Diatom cell walls (or frustules) contain silica. The cell wall plays a role in cell shape, cell stability and development, and protection against environmental dangers.Cell wall http://purl.uniprot.org/locations/41 The prokaryotic outer cell membrane is the selectively permeable membrane which separates the prokaryotic periplasm from its cell surroundings. Traditionally only Gram-negative bacteria were thought of as having an outer membrane, but recent work has shown some Actinobacteria, including Mycobacterium tuberculosis, as well as at least 1 archaea (Ignicoccus hospitalis) have a cell outer membrane.Cell outer membrane http://purl.uniprot.org/locations/40 The S-layer is a paracrystalline protein thin layer attached to the outermost portion of the cell wall. Found in some bacteria and common in archaea where it can constitute the only cell wall structure outside the plasma membrane. In Gram-negative bacteria, the S-layer is directly attached to the outer membrane. In Gram-positive bacteria, the S-layer is attached to the peptidoglycan layer. The S-layer may protect the cell from aggressions such as phagocytosis, harmful enzymes, etc. It also allows bacteria to adhere to host cells or other environmental surfaces and to maintain shape and envelope rigidity.S-layer http://purl.uniprot.org/locations/262 A fimbrium or pilus is a hair-like, non-flagellar, polymeric filamentous appendage that extend from the bacterial or archaeal cell surface, such as type 1 pili, P-pili, type IV pili or curli. Pili perform a variety of functions, including surface adhesion, motility, cell-cell interactions, biofilm formation, conjugation, DNA uptake, and twitching motility.Fimbrium http://purl.uniprot.org/locations/113 http://purl.uniprot.org/locations/36The myelin membrane is the white matter coating our nerves, enabling them to conduct impulses between the brain and other parts of the body. It consists of a layer of proteins packed between two layers of lipids. This specialized cell membrane is produced by oligodendrocytes in the central nervous system, and Schwann cells in the peripheral nervous system. Myelin sheaths wrap themselves around axons, the threadlike extensions of neurons that make up nerve fibers. Each oligodendrocyte can myelinate several axons. The major function of myelin is to increase the velocity of propagation of nerve impulses.Myelin membraneA specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.Synaptic cell membraneThe cell membrane is the selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the cell inner membrane in prokaryotes with 2 membranes.Cell membraneIn a chemical synapse, specialized area of the membrane that receives a signal (binds neurotransmitter) from the presynaptic cell and responds via depolarization or hyperpolarization. The postsynaptic membrane is separated from the presynaptic membrane by the synaptic cleft.Postsynaptic cell membraneThe portion of the cell membrane surrounding the dendritic spine, a small, club-like cell protrusion from neuronal dendrites that form the postsynaptic component of most excitatory synapses in the brain.Dendritic spine membraneIn a chemical synapse, the presynaptic membrane is the cell membrane of an axon terminal that faces the receiving cell. The postsynaptic membrane is separated from the presynaptic membrane by the synaptic cleft.Presynaptic cell membraneThe sarcolemma is a specialized membrane which surrounds striated muscle fiber cells. It consists of a lipid bilayer typical of a plasma membrane and a thin outer coat of polysaccharide material, called glycocalyx, that contacts the basement membrane and allows the cell to anchor into the tissues that build and support muscle fibers.Sarcolemma The cytoskeleton is a dynamic three-dimensional filamentous structure in the cytoplasm. Its roles include maintenance of cell shape, cell movement (in eukaryotes), cytokinesis, and the organization of organelles or organelle-like structures within the cell. The cytoskeleton includes microfilaments (actin-like proteins), microtubules (tubulin-like proteins), the intermediate filaments (mostly in eukaryotes) and the MinD-ParA proteins, which appear to be unique to prokaryotes.Cytoskeleton http://purl.uniprot.org/locations/90 The flagellum of Bacteria is a long hair-like cell surface appendage. The flagellar apparatus consists of the flagellar filament made of polymerized flagellin (the propeller), the hook-like structure near the cell surface (the universal joint) and the basal body (the engine) which is a rod and a system of rings embedded in the cell envelope. The basal body and the hook anchor the whip-like filament to the cell surface. The flagellum is a rotating structure whose switches propels the cell through a liquid medium.Bacterial flagellum http://purl.uniprot.org/locations/307 A specialized, membrane-bound bacterial organelle that envelops nanometer-sized crystals of magnetic iron minerals. They form linear chains at midcell along the cellular motility axis.Magnetosome http://purl.uniprot.org/locations/510The magnetosome membrane.Magnetosome membrane The thylakoid is a membranous cellular structure containing the photosynthetic pigments, reaction centers and electron-transport chain. In chloroplast, thylakoids stack up to form the grana or stay as single cisternae and interconnect the grana. Thylakoid, where photosynthesis occurs, are found in chloroplasts, cyanelles and in photosynthetic bacteria where they are the extensive invaginations of the plasma membrane.Thylakoid http://purl.uniprot.org/locations/450 Gas vesicles are rigid hollow structures found in five phyla of the Bacteria and two groups of the Archaea, but mostly restricted to planktonic microorganisms, in which they provide buoyancy. By regulating their relative gas vesicle content, aquatic microbes are able to perform vertical migrations. The gas vesicle is impermeable to liquid water, but is highly permeable to gases and is normally filled with air. Two proteins have been shown to be present in the gas vesicle: GVPa, which makes the ribs that form the structure, and GVPc, which binds to the outside of the ribs and stiffens the structure against collapse.Gas vesicle http://purl.uniprot.org/locations/125The membrane surrounding a gas vesicle.Gas vesicle membrane The anammoxosome is a large intracytoplasmic compartment bounded by a single bilayer, ladderane-lipid-containing membrane present in bacteria that perform anaerobic ammonium oxidation (anammox). This organelle is the site of the anammox process, in which nitrite is used as the electron acceptor in the conversion of ammonium to dinitrogen (N2) gas and water. Anammox bacteria belong to the phylum Planctomycetes and are recognized as major players in the global nitrogen cycle.Anammoxosome http://purl.uniprot.org/locations/491The membrane of the anammoxosome, a single bilayer membrane that contains unusual lipids, i.e. the so-called ladderane lipids, which appear to be unique for anammox bacteria.Anammoxosome membrane The chlorosome is a photosynthetic light-harvesting complex found in anoxygenic green bacteria. Chlorosomes are flattened ellipsoidal organelles appressed to the cytoplasmic face of the cell membrane. They typically contain highly aggregated bacteriochlorophyll c, d, or e (Bchl), a small amount of Bchl a, carotenoids, quinones, and occasionally wax esters. The chlorosome envelope of green sulfur bacteria is an asymmetric membrane containing galactolipids with the galactosyl moieties exposed on the outer surface. The farnesyl tails of the BChl molecules within the chlorosome probably comprise the inner leaflet of this membrane.Chlorosome http://purl.uniprot.org/locations/59 The nucleoid is the prokaryotic pseudocompartment formed by the chromatin-dense area. This region, which is functionally equivalent to the eukaryotic nucleus, is not surrounded by a membrane.Nucleoid http://purl.uniprot.org/locations/187 Bacterial microcompartments (BMC) are proteinaceous polyhedral shells that encapsulate enzymes. The selectively permeable organelles protect their contents from the cytoplasm and/or the cytoplasm from reactants in their interior. The best characterized BMC is the carboxysome, which encapsulates RuBisCO and carbonic anhydrase, and enhances autotrophic CO(2) fixation. Other characterized BMCs encapsulate enzymes involved in ethanolamine or propanediol degradation; both pathways make toxic intermediates. Artifical BMCs can be expressed and filled with cargo proteins for biotechnological uses. BMCs are found in many bacterial phyla; in most cases their cargo is unknown.Bacterial microcompartment Carboxysomes are bacterial microcompartments in which ribulose bisphosphate carboxylase (RuBisCO)-mediated CO(2) fixation occurs. The cytoplasmic polyhedral inclusion bodies are surrounded by a thin protein coat. They enhance autotrophic CO(2) fixation in air by increasing the CO(2) concentration around RuBisCO, thus reducing its reaction with O(2), a competing substrate. They contain carbonic anhydrase as part of the CO(2) concentration mechanism.Carboxysome http://purl.uniprot.org/locations/34 http://purl.uniprot.org/locations/544 Proteinaceous polyhedral shells that encapsulate enzymes. The selectively permeable organelles protect their contents from their surrounding milieu and/or the milieu from reactants in their interior. The self-assembling, 25-42 nm nanocompartment shell, unlike larger bacterial microcompartments, is made of only 1 protein, and has only a few proteins inside. Shells 25 nm in diameter are made of 60 monomers, shells 32 nm are made of 180 monomers, while shells 42 nm in diameter are made of 240 monomers with T=1, T=3 or T=4 icosahedral symmetry respectively. The shell protein has an HK97-like fold and probably evolved from a viral protein. Artificial encapsulin nanocompartments can be expressed and filled with cargo proteins for biotechnological uses. They are found in many bacterial and a few archaeal phyla. In anammox bacteria they may be located inside the anammoxosome.Encapsulin nanocompartment http://purl.uniprot.org/locations/550 Spores are hardy unicellular units used by various bacteria, fungi, plants and protozoa to allow them to remain dormant during long periods of time and under often unfavorable conditions.Spore Spore Protein found in the spore core. The core also called spore matrix is the central part of the spore and contains normal cell structures, such as DNA, proteins and ribosomes, but is metabolically inactive.Spore core http://purl.uniprot.org/locations/253 Protein associated with the membrane that surrounds the center or core of a spore, often called spore inner membrane in bacterial spores.Spore membrane http://purl.uniprot.org/locations/363 Protein found in the spore wall. The spore wall is the main element of the spore's resistance to environmental stress. It is usually composed of several layers of different sugar polymers like mannans and glucans which are associated to glycoproteins. The composition, structure and number of layers are very different between bacteria, plants, protozoans or fungi.Spore wall http://purl.uniprot.org/locations/254 Protein found in the spore cortex. The spore cortex is a loosely cross-linked peptidoglycan layer localized between the spore core and the outer membrane or cortex membrane of bacterial mature spores. The cortex maintains heat resistance and dormancy.Spore cortex http://purl.uniprot.org/locations/364 Protein associated with the spore outer membrane. The outer membrane, also called the cortex membrane, is a membrane localized between the cortex and the inner layer of the coat of bacterial mature spores.Spore outer membrane http://purl.uniprot.org/locations/365 Protein found in the spore coat. The spore coat is the thick layer found beneath the perispore of some eukaryotic spores and bacterial mature spores. It is made up of highly cross-linked keratin and layers of specific proteins. The coat is composed of several electron-dense and lamella-like layers, differing between species.Spore coat http://purl.uniprot.org/locations/366 Protein found in the perispore. The perispore corresponds to the outer surface layer of mature bacterial spores and eukaryotic spores. The perispore, also called perine or exosporium, represents the primary contact surface between the spore and environment/host and is a site of spore antigens.Perispore http://purl.uniprot.org/locations/367 http://purl.uniprot.org/locations/539 Philippe Le Mercier Coccus bacteria: two membranes (Gram-)

SBP Full

{{< sbp-full Animal_cells >}}
Protein located outside the cell membrane(s).Secreted The extracellular space is the space outside of the cell membrane but part of a multicellular organism. The term is typically used for a secreted protein that remains associated with the cell, e.g. as part of the extracellular matrix. It is not used for a protein that is secreted into the blood stream (or other body fluids) of eukaryotic, multicellular organisms, such as insulin or fibroblast growth factors.Extracellular space The extracellular matrix (ECM) is a vague term used to refer to all the material surrounding cells in a multicellular organism, except circulating fluids such as blood or lymph. In some cases, the ECM accounts for more of the organism's bulk than its cells. In plants, arthropods and fungi the ECM is primarily composed of nonliving material such as cellulose or chitin. In vertebrates the ECM consists of a complex network including the basement membrane, collage, elastin, proteoglycans and hyaluronan.Extracellular matrix http://purl.uniprot.org/locations/111 http://purl.uniprot.org/locations/112 Exosomes are 30-120 nm microvesicles of endocytic origin secreted by most cell types and found in abundance in body fluids, including blood, saliva, urine, and breast milk. They contain various molecular constituents of their cell of origin, including proteins and nucleic acids, and carry this cargo between diverse locations in the body. These microvesicles form by budding into the lumen of the multivesicular bodies (MVBs) and are released to extracellular fluids by fusion of MVBs with the plasma membrane.Extracellular exosome http://purl.uniprot.org/locations/466 http://purl.uniprot.org/locations/243 The cytoplasm is the content of a cell within the plasma membrane and, in eukaryotics cells, surrounding the nucleus. This three-dimensional, jelly-like lattice interconnects and supports the other solid structures. The cytosol (the soluble portion of the cytoplasm outside the organelles) is mostly composed of water and many low molecular weight compounds. In eukaryotes, the cytoplasm also contains a network of cytoplasmic filaments (cytoskeleton).Cytoplasm The cytosol is the unstructured aqueous phase of the cytoplasm excluding organelles, membranes, and insoluble cytoskeletal components.Cytosol http://purl.uniprot.org/locations/91 http://purl.uniprot.org/locations/86 The cell cortex is the cytoplasmic region under the cell membrane.Cell cortex http://purl.uniprot.org/locations/138 The perinuclear region is the cytoplasmic region just around the nucleus.Perinuclear region http://purl.uniprot.org/locations/198 The cytoskeleton is a dynamic three-dimensional filamentous structure in the cytoplasm. Its roles include maintenance of cell shape, cell movement (in eukaryotes), cytokinesis, and the organization of organelles or organelle-like structures within the cell. The cytoskeleton includes microfilaments (actin-like proteins), microtubules (tubulin-like proteins), the intermediate filaments (mostly in eukaryotes) and the MinD-ParA proteins, which appear to be unique to prokaryotes.Cytoskeleton Stress fibers are contractile actomyosin bundles found in non-muscle cells, in eukaryotes, mostly in animals. They are composed of bundles of 10 to 30 actin filaments (microfilaments), crosslinked by alpha-actinin, and non-muscle myosin. They are often anchored to focal adhesions, that connect the extracellular matrix to the actin cytoskeleton. Stress fibers play an essential role in cell contractility, governing cell morphology, adhesion, and migration. In non-motile cells, stress fibers are usually thick and relatively stable. By contrast, highly motile cells typically contain fewer, thinner and more dynamic stress fibers. Stress fibers can be divided into at least 4 different categories : dorsal and ventral stress fibers, transverse arcs and the perinuclear actin cap.Stress fiber http://purl.uniprot.org/locations/501 The microtubule organizing center (MTOC) is an intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules.Microtubule organizing center The centrosome is a microtubule organizing center (MTOC) responsible for the nucleation and organisation of microtubules. It is composed of two orthogonally arranged centrioles, each one having a barrel shaped microtubule structure, and their surrounding pericentriolar material (PCM).Centrosome The centriole is a barrel-shaped microtubule-based structure. A pair of centrioles, embedded in the so-called pericentriolar material, constitute the centrosome, a microtubule organizing center of an eukaryotic cell. Centrioles are barrel-shaped microtubule-based structures organized in a 9-fold radial symmetry. Centriolar microtubule arrays usually consist of triplet microtubules, although doublets or singlets are present in some species. Centrioles are structurally related to (and often interconvertible with) basal bodies, the organelles required for the assembly of a cilium or flagellum.Centriole http://purl.uniprot.org/locations/46 Centriolar satellites are nonmembranous, electron-dense and spherical cytoplasmic granules of about 70-100 nm in diameter, occurring around centrosomes in most vertebrate cell types. They contain a number of centrosomal proteins. Centriolar satellites have the ability to move along microtubules, toward their minus ends, i.e. toward centrosomes. Their number increase during interphase and decrease during mitosis.Centriolar satellite http://purl.uniprot.org/locations/485 http://purl.uniprot.org/locations/48 http://purl.uniprot.org/locations/484 http://purl.uniprot.org/locations/90 The cell membrane is the selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the cell inner membrane in prokaryotes with 2 membranes.Cell membrane http://purl.uniprot.org/locations/39 The outermost side of the cell.Cell surface http://purl.uniprot.org/locations/310 The nucleus is the most obvious organelle in any eukaryotic cell. It is a membrane-bound organelle surrounded by double membranes which contains most of the cell's genetic material. It communicates with the surrounding cytosol via numerous nuclear pores.Nucleus The nucleoplasm is a highly viscous liquid contained within the nucleus that surrounds the chromosomes and other subnuclear organelles. A network of fibers known as the nuclear matrix can also be found in the nucleoplasm.Nucleoplasm http://purl.uniprot.org/locations/190 The membrane surrounding the nucleus. This term is used when it is not known if the protein is found in or associated with the inner or outer nuclear membrane.Nucleus membrane http://purl.uniprot.org/locations/182 The nucleolus is a non-membrane bound nuclear compartment found in eukaryotic cells which is the site of ribosome biogenesis. The interphase nucleolus is organized around the tandemly repeated genes for preribosomal RNA (rRNA). It is composed of at least 2 sub-compartments: the dense fibrillar component (DFC, also called pars fibrosa) and the granular component (GC or pars granulosa). The DFC contains newly synthesized preribosomal RNA and a collection of proteins; the GC is made up of nearly completed preribosomal particles destined for the cytoplasm. In most metazoans, but generally not in lower eukaryotes, a third component, the fibrillar center (FC), can be seen. Plant and animal nuclei can contain more than one nucleolus.Nucleolus http://purl.uniprot.org/locations/188 Nuclear body is a collective term for several nuclear, extra-nucleolar, non-membrane-bound sub-compartments, including, but not limited to Cajal bodies, Gemini of Cajal bodies (gems), nuclear speckles and PML bodies. Nuclear bodies are visible as distinct spots in the nucleoplasm. They can vary in number and size depending on the cell line and the type of nuclear body.Nuclear body The nuclear Cajal bodies (CBs) are small subnuclear membraneless organelles present either free in the nucleoplasm and/or physically associated to specific regions of chromatin. CBs contain newly assembled small nuclear ribonucleoproteins (snRNPs) and small nucleolar ribonucleoproteins (snoRNPs) particles, which are involved in pre-mRNA splicing and in ribosomal RNA processing, respectively. Mammalian nucleus in interphase, show 2-6 CBs, as irregular, punctuate structures, which vary in size and shape and which are often juxtaposed to nucleoli. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called coiled body. Structures similar to CBs have been identified in the amphibian oocyte nucleus (called sphere organelles) and in insect (called endobodies). CBs are motile and dynamic structures. Both their protein and RNA-protein components can cycle continuously between CBs and other nuclear locations depending on the transcriptional state of the cell.Cajal body http://purl.uniprot.org/locations/31 The PML bodies are dynamic nuclear protein aggregates interspersed between chromatin. These punctate nuclear structures are call PML bodies because the PML gene is essential for their formation. These discrete nuclear foci, 0.2-1.0 micrometer wide, are present in most mammalian cell nuclei and typically number 1 to 30 bodies per nucleus, depending on the cell type, cell-cycle phase and differentiation stage. Recent evidence implies that, although they appear to be uniform, PML-NBs are structurally and functionally heterogeneous and are dynamic structures.PML body http://purl.uniprot.org/locations/465 Gems are nuclear bodies, often found paired or juxtaposed to Cajal bodies, called gems for "gemini of CBs". It is not clear if Cajal bodes and gems are distinct nuclear bodies or if they should be considered as two manifestations of the same structure.Gem http://purl.uniprot.org/locations/127 The nuclear speckles are small subnuclear membraneless organelles or structures, also called the splicing factor (SF) compartments that correspond to nuclear domains located in interchromatin regions of the nucleoplasm of mammalian cells. Protein found in speckles serves as a reservoir of factors that participate in transcription and pre-mRNA processing. Speckles appear, at the immunofluorescence-microscope level, as irregular, punctuate structures, which vary in size and shape. Usually 25-50 speckles are observed per interphase mammalian nucleus. At the electronic-microscope level, they are composed of heterogeneous mixture of electro-dense particles with diameters ranging from 20-25 nm and are called interchromatin granules clusters (IGCs). Speckles are dynamic structures. Both their protein and RNA-protein components can cycle continuously between speckles and other nuclear locations depending on the transcriptional state of the cell. Structures similar to nuclear speckles have been identified in the amphibian oocyte nucleus (called B snurposomes) and in Drosophila melanogaster embryos, but not in yeast.Nucleus speckle http://purl.uniprot.org/locations/186 http://purl.uniprot.org/locations/494 The nuclear lamina is a meshwork of intermediate filament proteins called lamins and lamin-binding proteins that are embedded in the inner nuclear membrane.Nucleus lamina http://purl.uniprot.org/locations/180 http://purl.uniprot.org/locations/191The inner membrane of the nucleus is the membrane which separates the nuclear matrix from the intermembrane space. In mammals, the inner nuclear membrane is associated with heterochromatin and the nuclear lamina.Nucleus inner membraneThe outer membrane of the nucleus is the membrane facing the cytoplasm. In mammals, the outer nuclear membrane is continuous in many places with the rough endoplasmic reticulum and is dotted with ribosomes.Nucleus outer membrane The mitochondrion is a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. The size and coding capacity of the mitochondrial DNA varies considerably in different organisms, and encodes rRNAs, tRNAs and essential mitochondrial proteins.Mitochondrion The matrix of a mitochondrion is the mitochondrion internal spaces enclosed by the inner membrane. Several of the steps in cellular respiration occur in the matrix due to its high concentration of enzymes.Mitochondrion matrix http://purl.uniprot.org/locations/170 The mitochondrial envelope comprises the inner and outer mitochondrial membrane including the intermembrane space.Mitochondrion envelope The membrane surrounding a mitochondrion. This term is used when it is not known if the protein is found in or associated with the inner or outer mitochondrial membrane.Mitochondrion membrane The outer membrane of a mitochondrion is the mitochondrial membrane facing the cytoplasm.Mitochondrion outer membrane http://purl.uniprot.org/locations/172 The inner membrane of a mitochondrion is the membrane which separates the mitochondrial matrix from the intermembrane space.Mitochondrion inner membrane http://purl.uniprot.org/locations/168 http://purl.uniprot.org/locations/171 http://purl.uniprot.org/locations/167 http://purl.uniprot.org/locations/173 The endoplasmic reticulum (ER) is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products. The membrane is a continuation of the outer nuclear membrane, it encloses the cytosol cisternal spaces (or internal lumen), which are continuous with the nuclear periplasmic space. The ER sustains many general functions, including protein synthesis, protein modification, protein folding, insertion of membrane proteins, sequestration of calcium, production of phospholipids and steroids and transport of proteins destined for membranes and secretion.Endoplasmic reticulum The smooth endoplasmic reticulum (SER) is the portion of the ER which is free of ribosomes.Smooth endoplasmic reticulum http://purl.uniprot.org/locations/248The membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membrane The rough endoplasmic reticulum (RER) is the portion of the ER which is covered with ribosomes.Rough endoplasmic reticulum http://purl.uniprot.org/locations/235The membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane http://purl.uniprot.org/locations/95The membrane surrounding the endoplasmic reticulum (ER). The endoplasmic reticulum is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products.Endoplasmic reticulum membraneThe membrane surrounding the microsome.Microsome membraneThe membrane surrounding the smooth endoplasmic reticulum.Smooth endoplasmic reticulum membraneThe membrane surrounding the rough endoplasmic reticulum.Rough endoplasmic reticulum membrane The Golgi apparatus is a series of flattened, cisternal membranes and similar vesicles usually arranged in close apposition to each other to form stacks. In mammalian cells, the Golgi apparatus is juxtanuclear, often pericentriolar. The stacks are connected laterally by tubules to create a perinuclear ribbon structure, the 'Golgi ribbon'. In plants and lower animal cells, the Golgi exists as many copies of discrete stacks dispersed throughout the cytoplasm. The Golgi is a polarized structure with, in most higher eukaryotic cells, a cis-face associated with a tubular reticular network of membranes facing the endoplasmic reticulum, the cis-Golgi network (CGN), a medial area of disk-shaped flattened cisternae, and a trans-face associated with another tubular reticular membrane network, the trans-Golgi network (TGN) directed toward the plasma membrane and compartments of the endocytic pathway. The Golgi apparatus receives the entire output of de novo synthesized polypeptides from the ER, and functions to posttranslationally process and sort them within vesicles destined to their proper final destination (e.g. plasma membrane, endosomes, lysosomes).Golgi apparatus The trans-Golgi network is a highly dynamic series of interconnected tubules and vesicles at the trans face of the Golgi stack. The trans-Golgi network functions in the processing and sorting of glycoproteins and glycolipids at the interface of the biosynthetic and endosomal pathways. The generation and maintenance of apical and basolateral membranes rely on sorting events that occur in the TGN.trans-Golgi network http://purl.uniprot.org/locations/266The membrane surrounding the trans-Golgi network.trans-Golgi network membrane The Golgi stack consist of a series of flattened curved and parallel series saccules, called cisternae or dictyosomes, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.Golgi stack http://purl.uniprot.org/locations/135The membrane surrounding the Golgi stack.Golgi stack membrane The cis-Golgi network is an extensive tubulovesicular network bound to the cis face of the Golgi stack and which function is to receive process the biosynthetic output from the ER.cis-Golgi network http://purl.uniprot.org/locations/67The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membrane http://purl.uniprot.org/locations/132The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network.cis-Golgi network membraneThe membrane surrounding the Golgi apparatus.Golgi apparatus membraneThe membrane surrounding the Golgi stack.Golgi stack membraneThe membrane surrounding the trans-Golgi network.trans-Golgi network membrane A cell projection is a cell protrusion such as pseudopodium, filopodium, lamellipodium, growth cone, flagellum, acrosome, axon, or bacterial comet tail. These membrane-cytoskeleton-coupled processes are involved in many biological functions, such as cell motility, cancer-cell invasion, endocytosis, phagocytosis, exocytosis, pathogen infection, neurite extension and cytokinesis.Cell projection The podosome is a ring-like cell protrusion which mediates cell-extracellular matrix interactions. Podosomes are composed of an actin-bundle core, flanked by a ring containing adhesion proteins connected to the core via dome-like radial actin fibers. Podosomes are rich in actin filaments, matrix-degrading enzymes, focal adhesion molecules and molecules involved in vesicle trafficking. These structures protrudes into the extracellular matrix and are essential for invasion and metastasis. Classical podosomes are highly dynamic structures formed by cell types of monocytic origin, such as macrophages, dendritic cells, and osteoclasts.Podosome http://purl.uniprot.org/locations/295 The filopodium is a thin, tubular, finger-like cell protrusion filled with straight bundled, crosslinked actin filaments having their barbed ends directed towards the cell membrane. Filopodium are observed at the advancing front of the migrating cell and are implicated in cell motility as well as in cell-substrate adhesion. Filopodia explore the environment and form nascent adhesive structures in response to external signaling cues. These long and highly dynamic protrusions, which can extend and retract, are involved in mesenchymal migration. They are observed in many cell types, such as amoebae, keratinocytes, fibroblasts and in neurite growth cones.Filopodium http://purl.uniprot.org/locations/286 The invadopodium is a localized and persitent cell protrusion similar to the highly dynamic podosome, but larger. These structures protrudes into the extracellular matrix. Invadopodial protrusions are enriched in integrins, tyrosine kinase signaling machinery, soluble and membrane proteases including matrix metalloproteases, actin and actin-associated proteins. Essential for physiological and pathological cell invasion and metastasis these structures are involved in focalized degradation of the extracellular matrix. Invadopodia form underneath the cell body, often close to the nucleus and proximal to the Golgi complex, and are rarely found at the cell periphery. Their half-life is quite extended. As invadopodia and podosomes are similar in appearance, location and composition, it is likely that a thin line separates these two entities in time and function.Invadopodium http://purl.uniprot.org/locations/148 The cilium is a cell surface projection found at the surface of a large proportion of eukaryotic cells. The two basic types of cilia, motile (alternatively named flagella) and non-motile, collectively perform a wide variety of functions broadly encompassing cell/fluid movement and sensory perception. Their most prominent structural component is the axoneme which consists of nine doublet microtubules, with all motile cilia - except those at the embryonic node - containing an additional central pair of microtubules. The axonemal microtubules of all cilia nucleate and extend from a basal body, a centriolar structure most often composed of a radial array of nine triplet microtubules. In most cells, basal bodies associate with cell membranes and cilia are assembled as 'extracellular' membrane-enclosed compartments.Cilium The basal body is a barrel-shaped microtubule-based structure required for the formation of cilia. Basal bodies, structuraly related to and often interconvertible with centrioles, serves as a nucleation site for axoneme growth.Cilium basal body http://purl.uniprot.org/locations/87 The cilium axoneme is the most prominent structural component of the cilium. It consists of nine doublet microtubules, with all motile cilia - except those at the embryonic node - containing an additional central pair of microtubules. The axonemal microtubules of all cilia nucleate and extend from a basal body, a centriolar structure most often composed of a radial array of nine triplet microtubules. In most cells, basal bodies associate with cell membranes and cilia are assembled as 'extracellular' membrane-enclosed compartments.Cilium axoneme http://purl.uniprot.org/locations/304 http://purl.uniprot.org/locations/66 http://purl.uniprot.org/locations/280 The hydrogenosome is a redox organelle of anaerobic unicellular eukaryotes which contains hydrogenase and produces hydrogen and ATP by glycolysis. They are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Most hydrogenosomes lack a genome, but some like that of the anaerobic ciliate Nyctotherus ovalis, have retained a rudimentary genome.Hydrogenosome http://purl.uniprot.org/locations/145The membrane surrounding the hydrogenosome, a redox organelle found in anaerobic unicellular eukaryotes.Hydrogenosome membrane The peroxisome is a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions. Contains mainly peroxidases, several other oxidases and catalase. The catalase regulates the contents of the produced toxic hydrogen peroxide thus protecting the cell. Beta-oxidation of fatty acids is another major function of peroxisomes. In plants and fungi this degradation occurs only in this cellular compartment.Peroxisome http://purl.uniprot.org/locations/204The membrane surrounding the the glycosome, a specialized peroxisome found in all members of the protist order Kinetoplastida examined.Glycosome membraneThe membrane surrounding the glyoxysome, a plant peroxisome, especially found in germinating seeds, involved in the breakdown and conversion of fatty acids to acetyl-CoA for the glyoxylate bypass.Glyoxysome membraneThe membrane surrounding a peroxysome.Peroxisome membrane The melanosome is a melanin-containing organelle found in melanocytes and melanophores. Fish and amphibians possess specialized cells, called melanophores, which contain hundreds of melanin-filled pigment granules, termed melanosomes. The sole function of these cells is pigment aggregation in the center of the cell or dispersion throughout the cytoplasm. This alternative transport of pigment allows the animal to effect color changes important for camouflage and social interactions. Melanophores transport their pigment in response to extracellular cues: neurotransmitters in the case of fish and hormonal stimuli in the case of frogs. In both cases, melanosome dispersion is induced by elevation of intracellular cAMP levels, while aggregation is triggered by depression of cAMP. The regulatory mechanisms downstream of these second-messengers are poorly understood. Mammalian melanocytes also produce melanosomes but, unlike melanophores, pigment in these cells is transported to the cell periphery for subsequent exocytosis to surrounding epithelial cells.Melanosome http://purl.uniprot.org/locations/161The membrane surrounding a melanosome.Melanosome membrane The organellar chromatophore is the photosynthetic inclusion found in Paulinella species, which are photosynthetic thecate amoeba. It probably derives from a different endosymbiotic event than that which led to all other plastids. Houses the machinery necessary for photosynthesis and CO(2) fixation and may also be able to make a few amino acids, some fatty acids and a few cofactors. They are surrounded by 2 membranes, between which is found a residual peptidoglycan wall, and contain thylakoids.Organellar chromatophore http://purl.uniprot.org/locations/351One of the membranes of an organellar chromatophore. This term is used when it is not known with which membrane (outer membrane, inner membrane or thylakoid) a protein is associated. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore membraneThe organellar chromatophore thylakoid membrane is an internal system of interconnected membranes that house the complexes which carry out the light reactions of photosynthesis. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore thylakoid membraneThe organellar chromatophore inner membrane is the membrane which separates the chromatophore stroma from the intermembrane space. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore inner membraneThe organellar chromatophore outer membrane is the organellar chromatophore membrane facing the cytoplasm. Found exclusively in Paulinella species, which are photosynthetic thecate amoeba.Organellar chromatophore outer membrane A contractile vacuole (CV) complex is a membrane-bound osmoregulatory organelle of fresh water and soil amoebae and protozoa which segregates excess cytosolic water, acquired osmotically, and expel it to the cell exterior, so that the cytosolic osmolarity is kept constant under a given osmotic condition. Depending on the organism, the CV complex (CVC) shows different degrees of specialization of its tubular and vesicular elements. In the most elaborate CVCs of certain ciliates, e.g. Paramecium, a central vacuole, the contractile vacuole or cisterna, is surrounded by radially oriented ampullae or radial arms. These ampullae are connected to a network of channels. Excess cytosolic water, acquired osmotically, is segregated by the radial arms and enters the vacuole, so that the vacuole swells (the fluid-filling phase). The vacuole then rounds (the rounding phase) and the radial arms sever from the vacuole. The vacuole membrane then fuses with the plasma membrane at the pore region and the pore opens. The vacuole shrinks as its fluid is discharged through the pore (the fluid-discharging phase). The pore closes when the fluid has been discharged. The radial arms then reattach to the vacuole, so that the vacuole swells again as the fluid enters from the arms (the next fluid-filling phase).Contractile vacuole http://purl.uniprot.org/locations/73The membrane surrounding a contractile vacuole. A contractile vacuole (CV) complex is a membrane-bound osmoregulatory organelle of fresh water and soil amoebae and protozoa which segregates excess cytosolic water, acquired osmotically, and expel it to the cell exterior, so that the cytosolic osmolarity is kept constant under a given osmotic condition.Contractile vacuole membrane The autophagosome is a double membrane vesicle involved in the degradation of long-lived proteins, unnecessary or damaged organelles as well as other cellular constituents such as lipids or carbohydrates. Crescent-shape isolation membranes or phagophores can sequester cytoplasm and organelles giving rise to autophagosomes. The outer membrane of the autophagosomes then fuse with vacuoles and/or lysosomes and the inner membrane vesicles (termed autophagic bodies) are released into the vacuole/lysosome lumen. These vesicles are then lysed and the contents are degraded by resident hydrolases.Autophagosome http://purl.uniprot.org/locations/23The membrane surrounding the autophagosome.Autophagosome membrane COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle http://purl.uniprot.org/locations/75The membrane surrounding a COPI-coated vesicle. COPI-coated vesicles mediate the vesicular transport of cargo such as proteins. COPI-coated vesicles are believed to bud from the cis-cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi back to the ER (retrograde), and govern the flow pattern of materials within the Golgi stack. COPI is composed of the coatomer, which is a seven-subunit protein complex that participates in the formation of Golgi-derived coated vesicles. Evidence has also been presented for anterograde intra-Golgi transport mediated by COPI in yeast and mammals.COPI-coated vesicle membrane COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle http://purl.uniprot.org/locations/77The membrane surrounding a COPII-coated vesicle. COPII-coated vesicles mediate the vesicular transport of cargo such as proteins. COPII-coated vesicles are believed to bud from the endoplasmic reticulum be involved in the anterograde transport between the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi intermediate compartment, where they fuse and release their contents (anterograde transport). The COPII coat has five main functional components that are highly conserved in all eukaryotic cells.COPII-coated vesicle membrane The ER-Golgi intermediate compartment is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites. The ERGIC mediates transport between the endoplasmic reticulum and the Golgi and is the first anterograde/retrograde sorting station in the secretory pathway. ERGIC has not been observed in yeast and plants.Endoplasmic reticulum-Golgi intermediate compartment http://purl.uniprot.org/locations/98The membrane surrounding the ER-Golgi intermediate compartment, which is a collection of tubulovesicular membrane clusters in the vicinity of ER exit sites.Endoplasmic reticulum-Golgi intermediate compartment membrane Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface. They also receive newly synthesised proteins destined for vacuolar/lysosomal compartments. In certain cell types, endosomal multivesicular bodies may fuse with the cell surface in an exocytic manner. These released vesicles are called exosomes.Endosome Late endosomes are pleiomorphic with cisternal, tubular and multivesicular regions. They are found in juxtanuclear regions and concentrated at the microtubule organizing center. They are an important sorting station in the endocytic pathway. Recycling to the plasma membrane and to the Golgi occurs in late endosomes. More acidic than early endosomes they are also loaded more slowly in a range of 4 to 30 minutes depending on the cell type. They can be distinguished from lysosome for their enrichment in M6PR.Late endosome http://purl.uniprot.org/locations/152The membrane surrounding the late endosomes.Late endosome membrane Early endosomes form a tubulovesicular network spread throughout the cortical cytoplasm of the cell. Early endosomes are the primary sorting station in the endocytic pathway from which endocytosed molecules can be recycled back to the cell membrane or targeted to degradation in the lysosomes. Loaded by endocytosed molecules in 1 to 4 minutes, their acidic luminal pH around 6.0 allows ligand release from recycling receptors.Early endosome http://purl.uniprot.org/locations/94The membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membrane The multivesicular bodies are a type of late endosome containing internal vesicles formed following the inward budding of the outer endosomal membrane. The contents of the MVBs are then released into the lysosome lumen. The proteins found in the limiting membrane of MVBs are recycled to other compartments.Multivesicular body http://purl.uniprot.org/locations/174The membrane surrounding the multivesicular bodies.Multivesicular body membrane Clathrin coated vesicles (CCVs) mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle http://purl.uniprot.org/locations/70The membrane surrounding a clathrin-coated vesicle (CCV). CCVs mediate the vesicular transport of cargo such as proteins between organelles in the post-Golgi network connecting the trans-Golgi network, endosomes, lysosomes and the cell membrane. CCVs that bud from the cell membrane reveal a striking polyhedral pattern reminiscent of a fullerene which arises from the outermost protein in the coat, clathrin. Clathrin assembles from three-legged individual components called triskelions to form a polygonal lattice around the vesicle. Clathrin is a large heterohexameric protein complex composed of three heavy chains and three light chains. Clathrin molecules self-assemble together to make a spherical clathrin lattice structure, a polyhedron made of regular pentagons and hexagons. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. The connection of the clathrin scaffold to the membrane is mediated by clathrin adaptors, which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes. Clathrin-associated adaptor protein (AP) complexes are a stoichiometric coat component of CCVs alongside clathrin itself, and are considered a major clathrin adaptor contributing the CCV formation.Clathrin-coated vesicle membrane http://purl.uniprot.org/locations/101The membrane surrounding the endosome. Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface.Endosome membraneThe membrane surrounding the late endosomes.Late endosome membraneThe membrane surrounding the recycling endosomes.Recycling endosome membraneThe membrane surrounding the early endosomes, which form a tubulovesicular network spread throughout the cortical cytoplasm of the cell.Early endosome membraneThe membrane surrounding the multivesicular bodies.Multivesicular body membrane The caveola is a small (apparently) uncoated pit mostly found in the cell membrane of many highly differentiated mammalian cells, such as adipocytes, endothelial cells and muscle cells. These flask-shaped invaginations are defined by the presence of caveolins and contains a subset of lipid-raft components, including cholesterol and sphingolipids. Caveolae each comprise a caveolar bulb with a diameter of 60-80 nm, connected to an opening of fairly constant diameter. Caveolae might exists as single pits or can form a cluster of caveolae with non-caveolar membrane between the pits. In many tissues, and particularly in adipocytes, multiple caveolae are arranged around a central vacuolar domain. In developing muscle fibres, multiple caveolae are connected by a single neck to the cell membrane, producing large chains of interconnected caveolae. Another structural feature of caveolae in certain endothelia is the presence of a stomatal diaphragm, which consists of a central density and radial spikes, in the neck of the caveolae. Mature caveolae might be assembled in the Golgi apparatus. Caveolae can flatten out into the cell membrane, thereby loosing their caveolar identity.Caveola http://purl.uniprot.org/locations/35 Coated pits are regions of the donor membrane where the assembly of the vesicle coat take place. The coat assembles from soluble protomers such as coat protein complex-I and coat protein complex-II. The components of the coat often define the intracellular sorting station, and contribute to both membrane deformation and local movement of the resulting transport intermediate following scission. During the first steps of the vesicle-mediated membrane transport, coated pits are internalized to form coated vesicles which transport proteins between distinct membrane-bound organelles.Coated pit Coated pits are regions of the cell membrane specialized in receptor-mediated endocytosis. Their cytoplasmic surface is coated with a bristlelike structure made of clathrin. During the first steps of endocytosis, clathrin-coated pits are internalized to form clathrin-coated vesicles which transport proteins from organelle to organelle.Clathrin-coated pit http://purl.uniprot.org/locations/69 http://purl.uniprot.org/locations/72 The lysosome is a membrane-limited organelle present in all eukaryotic cells, which contains a large number of hydrolytic enzymes that are used for degrading almost any kind of cellular constituent, including entire organelles. The mechanisms responsible for delivering cytoplasmic cargo to the lysosome/vacuole are known collectively as autophagy and play an important role in the maintenance of homeostasis.Lysosome http://purl.uniprot.org/locations/158The cytolytic granule membrane is the membrane surrounding a cytolytic granule.Cytolytic granule membraneThe membrane surrounding a lysosome.Lysosome membrane Cup-shaped invaginations of the cell membrane that subsequently close at their distal margins to form phagosomes during phagocytosis. By progression of its rim along the particle surface, this phagocytic cup envelops and eventually encloses the particle by separation of the phagosome membrane from the cell membrane. Filamentous actin accumulates between the outer and inner leaflet of the cup membrane and is most strongly enriched at the rim of the cup, the site of its protrusion.Phagocytic cup http://purl.uniprot.org/locations/473 The phagosome is a phagocytic cell-specific compartment. These large endocytic membrane-bound vesicles form upon ingestion by the cell of extracellular materials.Phagosome http://purl.uniprot.org/locations/206The membrane surrounding a phagosome.Phagosome membrane Focal adhesions are sites of tightest adhesion made to the underlying extracellular matrix by cells in culture. They serve a structural role, linking the ECM on the outside to the actin cytoskeleton on the inside. In addition, they are sites of signal transduction, initiating signaling pathways in response to adhesion. Focal adhesions are formed around a transmembrane core of an alpha-beta integrin heterodimer, which binds to a component of the extracellular matrix on its extracellular region, constitutes the site of anchorage of the actin cytoskeleton to the cytoplasmic side of the membrane, and mediates various intracellular signaling pathways.Focal adhesion http://purl.uniprot.org/locations/118 The lipid droplet is a dynamic cytoplasmic organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. Lipid droplets may play a role in lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.Lipid droplet http://purl.uniprot.org/locations/154 A chromaffin granule is a specialized secretory vesicle characteristic of chromaffin cells.Chromaffin granule http://purl.uniprot.org/locations/61The chromaffin granule membrane is the membrane surrounding a chromaffin granule, a specialized secretory vesicle characteristic of chromaffin cells.Chromaffin granule membrane Protein found in or associated with cytoplasmic granules.Cytoplasmic granule http://purl.uniprot.org/locations/281The membrane surrounding a cytoplasmic granule.Cytoplasmic granule membrane Philippe Le Mercier Animal cell